# Patent

## Title
Gene expression profiles to predict relapse of prostate cancer

## Abstract

The present disclosure provides a method for cancer relapse prediction that provides higher resolution grading than Gleason score alone. In particular, the method provides for prediction of prostate cancer relapse that correlates gene expression of each individual signature gene and deriving a prostate cancer gene expression (GEX) score in the plurality of prostate cancer tissue samples; and correlating said GEX score with the clinical outcome for each prostate carcinoma tissue sample. A set of signature genes is provided that encompasses all or a sub-combination of GI_2094528, KIP2, NRG1, NBL1, Prostein, CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B, and PROK1.

## Background
This application is a continuation application of U.S. application Ser. No. 13/035,797, filed Feb. 25, 2011, which is a continuation application of U.S. application Ser. No. 11/732,481, filed Apr. 2, 2007, now U.S. Pat. No. 7,914,988, which claims the benefit of priority to, U.S. Provisional Application Ser. No. 60/787,868, filed Mar. 31, 2006, the entire contents of which are incorporated herein by reference in their entireties.


FIELD
This invention relates generally to gene expression profiling and, more specifically, to relapse prediction and clinical management of prostate cancer.
BACKGROUND
Prostate cancer is the most common cancer in American men and is the second leading cause of cancer death. Progress in treating human prostate cancer has been hampered by the finding that histologically identical cancers can exhibit widely variant clinical behavior. For example, in some men diagnosed with prostate cancer, the disease progresses slowly with a prolonged natural history while in other patients, disease progression can be rapid and definitive local therapy can be ineffective. The uncertainty regarding the appropriate clinical management of prostate cancer in many patients is related to an incomplete and unclear understanding of the molecular and genetic changes involved in prostate cancer development and disease progression.
A variety of clinical models or nomograms have been developed to aid clinicians with pre-treatment risk assessment. For example, since 1988, the routine use of serum prostate-specific antigen (PSA) testing in men at risk for prostate cancer has led to more favorable disease characteristics at presentation (stage migration) and earlier diagnosis and treatment. Several investigators have used these clinical parameters to stratify patients into risk groups (low, intermediate, high) and to predict clinical outcomes (Nomograms). Despite these useful parameters, approximately 30% of patients with intermediate-risk prostate cancer fail standard treatment as evidenced by a rising serum PSA following definitive therapy. A better understanding of the molecular abnormalities that define these tumors at high risk for relapse is needed to help identify more precise biosignatures.
For patients newly diagnosed with prostate cancer, there are three well-defined predictors of disease extent and outcome following treatment. These factors are clinical tumor stage (T1-T4) by digital rectal examination, Gleason score of the diagnostic biopsy specimen and serum PSA level. However, each of these factors alone has not proven definitive in predicting disease extent and outcome for an individual patient. Clinical staging by digital rectal examination may underestimate the presence of extracapsular disease extension in 30-50% of patients. Although biopsy Gleason score may be helpful in predicting pathologic stage and outcome following treatment at either end of the spectrum (i.e. Gleason 2-4 or Gleason 8-10 tumors), it is not as helpful for the majority of patients who present with Gleason 5-7 disease. As risk assessment for patients newly diagnosed with prostate cancer continues to evolve, newer tools, such as genetic or molecular determinants are needed to better predict the behavior of an individual tumor.
A need exists for large-scale discovery, validation, and clinical application of mRNA biosignatures of disease and for methods of genomic analysis in patients with established clinical prostate cancer disease to predict disease outcomes. The present invention satisfies this need and provides related advantages as well.
BRIEF SUMMARY
The present invention provides a method for preparing a reference model for cancer relapse prediction that provides higher resolution grading than Gleason score alone. The method encompasses obtaining from different individuals a plurality of prostate carcinoma tissue samples of known clinical outcome representing different Gleason scores; selecting a set of signature genes having an expression pattern that correlates positively or negatively in a statistically significant manner with the Gleason scores; independently deriving a prediction score that correlates gene expression of each individual signature gene with Gleason score for each signature gene in said plurality of prostate carcinoma tissue samples; deriving a prostate cancer gene expression (GEX) score that correlates gene expression of said set of signature genes with the Gleason score based on the combination of independently derived prediction scores in the plurality of prostate cancer tissue samples; and correlating said GEX score with the clinical outcome for each prostate carcinoma tissue sample. A set of signature genes is provided that encompasses all or a sub-combination of GI—2094528, KIP2, NRG1, NBL1, Prostein, CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B, and PROK1. Also provided are methods for predicting the probability of relapse of cancer in an individual and methods for deriving a prostate cancer gene expression (GEX) score for a prostate carcinoma tissue sample obtained from an individual.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows the correlation between gene expression signature and Gleason score. 5-N, 6-N, 7-N and 8-N, correspond respectively to patient groups with Gleason score of 5, 6, 7 and 8 without relapse. 6-Y, 7-Y, 8-Y and 9-Y, correspond respectively to patient groups with Gleason score of 6, 7, 8 and 9 with relapse.
FIG. 2 shows a plot of percentage of relapse cases vs. the GEX score.
FIG. 3 shows a Receiver Operating Characteristic (ROC) curve for relapse prediction in prostate cancer. False positive is defined as a case with no relapse, but high score. The connected line shows the performance of GEX and the dotted line shows the performance of Gleason score.
FIG. 4 shows Kaplan-Maier analysis of relapse (N=71). X-axis: Time to relapse (days); Y-axis: Relapse free probability. (A) Relapse prediction based on expression signature, GEX>7.337, p=0.0044; (B) Relapse prediction based on Gleason score, Gleason score>7 (p=0.138)
FIG. 5 shows immunohistochemical stains of HOXC6 and Ki67 in tumor cells. Immunohistochemical stains for HOXC6 showed strong nuclear stains in the prostate cancer cells (A) whereas the normal adjacent glands (B) did not show any staining Ki67 showed variable nuclear stains in the tumor cells (C), but much less stain in the nearby normal prostate glands (D). All magnifications are 400×.
FIG. 6 shows FFPE-derived RNA metrics. Bioanalyzer traces for 10 FFPE-derived prostate cancer RNAs are shown. These traces represent the more marginal FFPEs. Ct was measured for a 90 bp amplicon from the RPL13a gene using SYBR Green detection. R2 represents the correlation between replicate DASL assays for the same cDNA run in parallel. Numbers in red identify samples with poor performance.
FIG. 7 shows sample QC (by qPCR) and array data quality assessment. Highly reproducible gene expression data are obtained with samples that have up to 8 cycle difference in qPCR (i.e.  ̃170-fold difference in “PCR-able” RNA input) for a housekeeping gene RPL13A. Samples are pre-qualified for array analysis by qPCR, using a Ct number of 28 as the cutoff.
FIG. 8 shows a plot of the distribution of survival p-values for various collections of signature genes selected among the following 7 genes: MKI67, GI—2094528, HOXC6, CCK, memD, FBP1, and CDC6. The same data is plotted in panels A and B but displayed with different scale on the y axis.
FIG. 9 shows Kaplan-Maier analysis of relapse (N=71) based on the GEX score derived from the following 7 genes: MKI67, GI—2094528, HOXC6, CCK, memD, FBP1, and CDC6. X-axis: Time to relapse (days); Y-axis: Relapse free probability.



DETAILED DESCRIPTION
This invention is directed to methods for gene expression profiling in cancer tissues and the identification of cancer diagnostic and prognostic biomarkers. In particular, the method of the invention allows for the establishment of a molecular signature based on identifying a correlation between the gene expression of each member of a set of signature genes in a cell population derived from prostate carcinoma tissue sample with the Gleason score corresponding to the tissue sample. It has been discovered that the molecular signature can be expressed as a combined score, termed the Gene Expression Score (“GEX score”), which allows for relapse prediction more sensitive than relapse prediction based solely on Gleason score. For each member of the set of signature genes that contribute to the GEX score, a highly reproducible correlation of gene expression, either positive or negative, with Gleason score can reproducibly be calculated and incorporated into the GEX score.
The present invention provides a method for establishing a model, also referred to as a “reference model,” for prostate relapse prediction against which any individual patient sample can be compared to predict relapse probability more accurately than Gleason score alone. The invention also provides a method for deriving a prostate cancer gene expression score by obtaining a cell population from a tissue sample obtained from an individual, calculating the GEX score in the tissue sample, and comparing the GEX score to an established model for relapse prediction. The invention also provides a set of signature genes for prostate cancer relapse prediction.
In a particular embodiment, the invention provides a method for preparing a model for cancer relapse prediction. This method comprises the following steps: (a) obtaining a plurality of cell populations from prostate carcinoma tissues representing different Gleason scores, wherein the clinical outcome corresponding to each of the prostate carcinoma tissues is known; (b) selecting a set of signature genes having an expression pattern that correlates positively or negatively with the Gleason scores in prostate cancer patients; (c) statistically deriving a prediction score for each signature gene in the plurality of cell populations, wherein the prediction score correlates gene expression of each individual signature gene with Gleason score; (d) statistically deriving a prostate cancer gene expression score by calculating the average of the independently derived prediction scores in the plurality of tissue samples, wherein the prostate cancer gene expression score correlates gene expression of the set of signature genes with the Gleason score; and (e) establishing a model for relapse prediction from the plurality of cell populations that describes the association between gene expression score and probability of relapse for prostate cancer.
In a particular embodiment, the invention provides a method for predicting the probability of relapse of prostate cancer in an individual by performing the steps of (a) providing expression levels for a collection of signature genes from a test individual; (b) deriving a score that captures the expression levels for the collection of signature genes; (c) providing a model comprising information correlating the score with prostate cancer relapse; and (d) comparing the score to the reference model, thereby determining the probability of prostate cancer relapse for the individual.
Signature genes of the invention, which are differentially expressed within prostate carcinomas and which are further positively or negatively correlated with Gleason score, are as follows: GI—2094528, KIP2, NRG1, NBL1, Prostein, CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B, and PROK1. Of the 21 signature genes, twelve are positively correlated with Gleason score: GI—2094528, CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD; and nine are negatively correlated with Gleason score: KIP2, NRG1, NBL1, Prostein, AZGP1, CCK, MLCK, PPAP2B, and PROK1.
The sensitivity and specificity of the molecular signature derived from these 21 signature genes, or subset thereof, has utility for patients undergoing prostate biopsy for diagnosis of carcinoma based on applicability of the methods described herein to diagnosis as well as prognosis through biopsy samples. Furthermore, the present invention enables the development of a diagnostic test that is technically simple and applicable for routine clinical use, and incorporation into existing prostate cancer nomograms (Group TTABPW, Nat Rev Genet 5:229-37 (2004); Ramaswamy, N Engl J Med 350:1814-6 (2004); Sullivan Pepe et al. J Natl Cancer Inst 93:1054-61 (2001)).
The articles “a” and “an” are used herein to refer to one or to more than one (i.e. to at least one) of the grammatical object of the article. By way of example, “an element” means one element or more than one element, unless explicitly indicated to the contrary.
“Prostate cancer” as used herein includes carcinomas, including, carcinoma in situ, invasive carcinoma, metastatic carcinoma and pre-malignant conditions.
As used herein the term “comprising” means that the named elements are essential, but other signature genes or claim elements may be added and still represent a composition or method within the scope of the claim. The transitional phrase “consisting essentially of” means that the claimed composition or method encompasses additional elements, including, for example, additional signature genes, that do not affect the basic and novel characteristics of the claimed invention. The transitional phrase “comprising essentially” means that the claimed composition or method encompasses additional elements, including, for example, additional signature genes or claim, that do not substantially affect the basic and novel characteristics of the claimed invention.
As used herein, the term “signature gene” refers to a gene whose expression is correlated, either positively or negatively, with disease extent or outcome or with another predictor of disease extent or outcome. A gene expression score (GEX) can be statistically derived from the expression levels of a set of signature genes and used to diagnose a condition or to predict clinical course. A “signature nucleic acid” is a nucleic acid comprising or corresponding to, in case of cDNA, the complete or partial sequence of a RNA transcript encoded by a signature gene, or the complement of such complete or partial sequence. A signature protein is encoded by or corresponding to a signature gene of the invention.
The term “relapse prediction” is used herein to refer to the prediction of the likelihood of cancer recurrence in patients with no apparent residual tumor tissue after treatment. The predictive methods of the present invention can be used clinically to make treatment decisions by choosing the most appropriate treatment modalities for any particular patient. The predictive methods of the present invention also can provide valuable tools in predicting if a patient is likely to respond favorably to a treatment regimen, such as surgical intervention, chemotherapy with a given drug or drug combination, and/or radiation therapy.
In the exemplified embodiments relating to cancer relapse prediction, the gene expression of 21 signature genes, or subsets thereof, differentially expressed in prostate cancer is correlated to Gleason scores. The Gleason grading system is based on the glandular pattern of the tumor. Gleason grade takes into account the ability of the tumor to form glands. A pathologist, using relatively low magnification, performs the histologic review necessary for assigning the Gleason grade. The range of grades is 1-5: 1, 2 and 3 are considered to be low to moderate in grade; 4 and 5 are considered to be high grade. The prognosis for a given patient generally falls somewhere between that predicted by the primary grade and a secondary grade given to the second most prominent glandular pattern. When the two grades are added the resulting number is referred to as the Gleason score. The Gleason Score is a more accurate predictor of outcome than either of the individual grades. Thus, the traditionally reported Gleason score will be the sum of two numbers between 1-5 with a total score from 2-10. It is unusual for the primary and secondary Gleason grade to differ by more than one, such that the only way that there can be a Gleason score 7 tumor is if the primary or secondary Gleason grade is 4. Because of the presence of grade 4 glandular patterns in tissue having Gleason score 7, these tumors can behave in a much more aggressive fashion than those having Gleason score 6. In a recent study of over 300 patients, the disease specific survival for Gleason score 7 patients was 10 years. In contrast, Gleason score 6 patients survived 16 years and Gleason 4-5 for 20 years. It is therefore clear that the prognosis for men with Gleason score 7 tumors is worse than for men with Gleason score 5 and 6 tumors. Under certain circumstances it is suggested that men with Gleason 7 tumors can be considered for clinical trials.
As disclosed herein, the gene expression score (GEX) derived from the expression levels of signature genes can be used to predict relapse of prostate cancer. A “GEX score” or “score” is a value that captures the expression levels for a collection of signature genes. Notably, making continuous analogy of Gleason score increased molecular resolution, especially at a Gleason Score between 7 and 8, in which relapse probability of patients can be stratified beyond the capability of the Gleason score alone because the GEX score provides a more sensitive predictor of relapse for prostate cancer, especially in this range. As disclosed in Example I below, a significant difference exists in the mean of the GEX score between GS7 patients who had relapse (GS7-Y) and those without relapse (GS7-N), making the GEX score a valuable source of information for the very patients faced with the most critical decision point along the Gleason score spectrum.
Furthermore, while it is established that Gleason score 7 tumors behave in a more aggressive fashion than do Gleason 5 and 6 tumors, it has been less clear whether or not it makes a difference if the primary or secondary pattern accounts for the Gleason score 4 grade. Some studies have shown Gleason 4+3 to be a worse prognostic sign than is Gleason 3+4 (where Gleason x+y represents Gleason score derived from primary grade “x” and secondary grade “y”). However, this has not always been the case and there are studies that find no difference between the two scores. To date, there had not been a prospective study that has attempted to answer this question and it has remained a controversial point. The present invention confirms that among Gleason score 7 patients, a primary Gleason score of 4 is consistent with a significantly higher relapse probability. Among the GS7 patients, 21 are (3+4) and 11 are (4+3), of which 1 and 4 are relapsed respectively (Exact Fisher test p=0.037). A mean GEX score of 7.236 and 7.305 for the two groups, respectively (p=0.071 for hypothesis testing increased GEX score for 4+3 patients) was obtained.
The ability to stratify individuals having a Gleason Score between 7 and 8 based on probability of relapse is significant because a Gleason score of 7 is a crucial decision point that necessitates seeking treatment as early as possible, considering therapies beyond surgery and radiation, and having frequent follow-ups.
Among the signature genes disclosed herein is MEMD, a cell adhesion molecule often found in metastasizing human melanoma cell lines. The intact cell adhesion function of MEMD can both favor primary tumor growth and represent a rate-limiting step for tissue invasion from vertical growth phase melanoma. Over expression of this molecule is associated with tumor invasion and nodal metastasis in esophageal squamous cell carcinoma. MEMD expression is up-regulated in low-grade prostate tumors and down-regulated in high-grade tumors and can play role in progression of prostate cancer. Also among the signature genes, HOXC6 was identified as a good signature for prediction of prostate cancer patient outcome, as was UBE2C, ubiquitin-conjugating enzyme E2C, which is highly expressed in various human primary tumors (e.g. anaplastic thyroid carcinomas) and has an ability to promote cell growth and malignant transformation. WNTSA: wingless-type MMTV integration site family, member 5A. The WNT gene family consists of structurally related genes which encode secreted signaling proteins, which have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. Wnt-5a serves as an antagonist to the canonical Wnt-signaling pathway with tumor suppressor activity in differentiated thyroid carcinomas and is involved in the response of malignant neuroblasts to retinoic acid. Up-regulation of Wnt-5a is a signature of the malignant phenotype of human squamous cell carcinoma and frequent up-regulation exists of WNTSA mRNA in primary gastric cancer. Increased expression of WNT5a is associated with cell motility and invasion of metastatic melanoma. The gene product of a further signature gene, PTTG1: pituitary tumor-transforming 1 has transforming activity in vitro and tumorigenic activity in vivo, and the gene is highly expressed in various tumors.
The invention also provides a collection of isolated prostate cancer signature genes consisting essentially of CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B and PROK1. The invention also provides a collection of isolated prostate cancer signature genes consisting of CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B and PROK1. The invention also provides a collection of isolated prostate cancer signature genes comprising CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B and PROK1.
The invention also provides a collection of isolated prostate cancer signature genes consisting essentially of GI—2094528, KIP2, NRG1, NBL1, Prostein, CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B and PROK1. The invention also provides a collection of isolated prostate cancer signature genes consisting of GI—2094528, KIP2, NRG1, NBL1, Prostein, CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B and PROK1. The invention also provides a collection of isolated prostate cancer signature genes comprising GI—2094528, KIP2, NRG1, NBL1, Prostein, CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B and PROK1.
The invention also provides a collection of isolated prostate cancer signature genes comprising any subset of the 21 genes set forth above including, for example, at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 of the 21 genes. The invention also provides a collection of isolated prostate cancer signature genes comprising CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK and PPAP2B. The invention also provides a collection of isolated prostate cancer signature genes comprising CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, and PROK1. The invention also provides a collection of isolated prostate cancer signature genes comprising CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, MLCK, and PPAP2B. The invention also provides a collection of isolated prostate cancer signature genes comprising CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, CCK, MLCK, PPAP2B and PROK1. The invention also provides a collection of isolated prostate cancer signature genes comprising CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, AZGP1, CCK, MLCK, PPAP2B and PROK1. The invention also provides a collection of isolated prostate cancer signature genes comprising CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, MEMD, AZGP1, CCK, MLCK, PPAP2B and PROK1. The invention also provides a collection of isolated prostate cancer signature genes comprising CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B and PROK1. The invention also provides a collection of isolated prostate cancer signature genes comprising CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B and PROK1. The invention also provides a collection of isolated prostate cancer signature genes comprising CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B and PROK1. The invention also provides a collection of isolated prostate cancer signature genes comprising CCNE2, CDC6, FBP1, HOXC6, MKI67, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B and PROK1. The invention also provides a collection of isolated prostate cancer signature genes comprising CCNE2, CDC6, FBP1, HOXC6, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B and PROK1. The invention also provides a collection of isolated prostate cancer signature genes comprising CCNE2, CDC6, FBP1, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B and PROK1. The invention also provides a collection of isolated prostate cancer signature genes comprising CCNE2, CDC6, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B and PROK1. The invention also provides a collection of isolated prostate cancer signature genes comprising CCNE2, CDC6, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B and PROK1. The invention also provides a collection of isolated prostate cancer signature genes comprising CCNE2, CDC6, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B and PROK1. The invention also provides a collection of isolated prostate cancer signature genes comprising CCNE2, CDC6, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B and PROK1. The invention also provides a collection of isolated prostate cancer signature genes comprising CCNE2, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B and PROK1. The invention also provides a collection of isolated prostate cancer signature genes comprising CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B and PROK1. All of the signature genes can be present in “isolated” form.
One skilled in the art can readily determine other combinations of signature genes sufficient to practice the inventions claimed herein. For example, based on the Pearson's correlation coefficient shown in Table 2 or Table 4, one skilled in the art can readily determine a sub-combination of prostate cancer signature genes suitable for methods of the invention. Those exemplary genes having lowest correlation can be excluded, with the remaining genes providing a sufficient collection of isolated prostate cancer signature genes suitable for relapse prediction of prostate cancer. For example, of those genes having a negative correlation, the CCK gene has the lowest correlation, and therefore removing the CCK gene is expected to have the least effect on overall accuracy of the GEX score. Similarly, of those genes having a positive correlation, removing the UBE2C is expected to have the least effect on overall accuracy of the GEX score. One skilled in the art can readily recognize these or other appropriate genes that can be omitted from the 21 identified prostate cancer signature genes and still be sufficient for methods of the invention.
Alternatively, one skilled in the art can remove any one or a few of the 21 identified prostate cancer signature genes so long as those remaining provide a sufficient statistical correlation for use in methods of the invention. Exemplary collections of prostate cancer signature genes include, for example, those set forth above and in the Examples. It is readily recognized by one skilled in the art that these listed combinations are merely exemplary and that any of a number of such combinations can readily be determined by one skilled in the art. For example, a sub-combination can be selected by removing the signature gene(s) with the weakest correlation, for example, GI—2094528, NRG1, Prostein or UBE2C based on overall correlation, including positive and negative; NRG1, Prostein or CCK based on the weakest negative correlation of the five signature genes having a negative correlation with GS. HOXC6 and RAMP have the strongest and second strongest, respectively, correlation to GS score of the sixteen signature genes and can therefore be included in a sub-combination based on this statistic. However, it is understood that, given the set of 21 signature genes, removal of a signature gene having a strong correlation, will likely not have a big impact on the overall GEX score. The correlations are set forth in Tables 2 and 4 and the skilled person understands that 0 indicates the absence of any linear relationship while correlations of −1 to +1 indicate, respectively a perfect negative (inverse) or positive (direct) relationship. Thus, the skilled person can easily determine, based on Tables 2 or 4, which signature genes have comparatively stronger or weaker correlations.
Additionally or alternatively, a ranking based on p-value correlations or other characteristics can be used to determine a sub-combination of the 21 genes for inclusion in a collection of signature genes or for use in a method set forth herein. An exemplary ranking is shown in Table 5. The genes are ranked in Table 5 according to the probability that each is predictive of prostate cancer relapse when evaluated alone or in combination with one or more other genes in the collection of 21 genes. For example, a GEX score based on the expression level of at least one gene in the collection of 21 genes that is predictive of prostate cancer relapse is most likely to include the expression level for the MKI67 gene. Thus, a GEX score based on the expression level of the MKI67 gene alone or in combination with at least one other gene in the collection of 21 genes has the highest probability of correctly predicting prostate cancer relapse. As a further example, a GEX score based on the expression level of at least two genes in the collection of 21 genes that is predictive of prostate cancer relapse is most likely to include the expression level for the MKI67 and GI—2094528 genes. Thus, a GEX score based on the expression level of the MKI67 and GI—2094528 genes exclusively or in combination with at least one other gene in the collection of 21 genes has the highest probability of correctly predicting prostate cancer relapse. Accordingly, collections of signature genes can be built up according to their sequential occurrence in Table 5 (for example, continuing beyond the two collections set forth above, are a set including MKI67, GI—2094528, and HOXC6; a set including MKI67, GI—2094528, HOXC6 and CCK; and so forth).
However, as described in further detail below, a GEX score determined from the expression level of any individual gene in Table 5 or any combination of 2 to 21 genes in Table 5 can be used to predict relapse of prostate cancer so long as the gene expression pattern for the particular gene or combination of genes is correlated with Gleason score. Thus, although the best combination of gene expression levels to include in a 7 gene GEX score for prediction of prostate cancer relapse is derived from the MKI67, GI—2094528, HOXC6, CCK, memD, FBP1, and CDC6 genes, a GEX score including gene expression levels for a variety of other 7 gene combinations are also predictive.
Thus, the invention provides a method of predicting prostate cancer relapse based on the expression patterns for any subset of the 21 genes set forth in Table 5 including, for example, at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 of the 21 genes. The invention also provides a method of predicting prostate cancer relapse based on the expression patterns for any subset of the set of genes consisting of MKI67, GI—2094528, HOXC6, CCK, memD, FBP1, and CDC6 including, for example, at least 1, 2, 3, 4, 5 or 6 of the 7 genes. Similarly, the invention provides a collection of isolated prostate cancer signature genes comprising any subset of the set of genes consisting of MKI67, GI—2094528, HOXC6, CCK, memD, FBP1, and CDC6 including, for example, at least 1, 2, 3, 4, 5 or 6 of the 7 genes.
The sensitivity and specificity of the molecular signature derived from the sets of signature genes provided by the invention provides specific and substantial utility for patients undergoing prostate biopsy for diagnosis of prostate carcinoma based on applicability of the methods described herein to diagnosis as well as prognosis through biopsy samples. Furthermore, the present invention enables the development of a diagnostic test that is technically simple and applicable for routine clinical use, and incorporation into existing prostate cancer nomograms (Group TTABPW, Nat Rev Genet 5:229-37 (2004); Ramaswamy, N Engl J Med 350:1814-6 (2004); Sullivan Pepe et al. J Natl Cancer Inst 93:1054-61 (2001)). Particularly useful, molecular signatures or reference models derived from signatures such as expression patterns are those that are at least as predictive of prostate cancer relapse as Gleason score in prostate cancer patients.
As described herein, archived tissue samples, in particular, formalin-fixed paraffin embedded tissue (FFPE) samples, are particularly useful for establishing a model for relapse prediction because they are generally supported by sufficient clinical follow-up data to allow retrospective studies that correlate gene expression with clinical outcome. By “archived tissue sample” herein is meant tissue samples that have been obtained from a source and preserved. Preferred methods of preservation include, but are not limited to paraffin embedding, ethanol fixation and formalin (including formaldehyde and other derivatives) fixation as are known in the art. The sample may be temporally “old”, e.g. months or years old, or recently fixed. For example, post-surgical procedures generally include a fixation step on excised tissue for histological analysis. There are numerous tissue banks and collections comprising exhaustive samples from all stages of a wide variety of disease states, including cancer. Recently developed methods disclosed in U.S. patent application Ser. No. 10/678,608, which is incorporated herein by reference in its entirety, have made it feasible to obtain robust and reproducible gene expression patterns from archived tissues, including formalin-fixed, paraffin-embedded (FFPE) tissues. This ability to access reliable information from archived tissues enabled the discovery that is, in part, the present invention.
In a further embodiment, the invention provides a method for deriving a prostate cancer gene expression score for an individual prostate carcinoma tissue sample by (a) selecting a set of signature genes having an expression pattern that correlates with Gleason scores in prostate cancer patients; (b) independently deriving a prediction score for each of a set of signature genes known to have an expression pattern that correlates with Gleason score in prostate cancer patients, wherein the prediction score correlates gene expression of each individual signature gene with Gleason score; and (c) deriving a prostate cancer gene expression score by calculating the average of said independently derived prediction scores, wherein said prostate cancer gene expression score correlates gene expression of said set of signature genes with Gleason score.
An exemplary gene expression score and method for determining the score are provided in Example I. The gene expression score of Example 1 is calculated from independently derived prediction scores by averaging. In particular embodiments, a gene expression score can be calculated from the independently derived prediction scores with different weights, rather than averaging. It will be understood that any score that is capable of correlating gene expression of individual signature genes with Gleason score can be used in the invention.
In a related yet distinct embodiment, the invention provides a method for predicting the probability of relapse of prostate cancer in an individual by performing the following steps: (a) selecting a set of signature genes having an expression pattern that correlates with Gleason scores in prostate cancer patients; (b) independently deriving a prediction score for each signature gene, wherein the prediction score correlates gene expression of each individual signature gene with Gleason score; (c) deriving a prostate cancer gene expression score by calculating the average of the independently derived prediction scores, wherein the prostate cancer gene expression score correlates gene expression of the set of signature genes with Gleason score (d) comparing the cancer gene expression score to a model to determine the probability of relapse.
The invention further provides a method for predicting the probability of cancer relapse in an individual by performing the following steps: (a) providing a gene expression score derived from independently determined expression levels for a plurality of signature genes in suspected prostate cancer tissue obtained from the individual; (b) providing a model derived from the gene expression scores for a plurality of other individuals and the relapse rates for the plurality of other individuals and (c) comparing the gene expression score to the model to determine the probability of relapse.
In a particular embodiment, the invention provides a method for predicting the probability of relapse of prostate cancer in an individual by performing the steps of (a) providing expression levels for a collection of signature genes from a test individual; (b) deriving a score that captures the expression levels for the collection of signature genes; (c) providing a model comprising information correlating the score with prostate cancer relapse; and (d) comparing the score to the reference model, thereby determining the probability of prostate cancer relapse for the individual.
In a further embodiment, the invention provides a method for predicting the probability of relapse of prostate cancer in an individual by performing the steps of (a) providing expression levels for a collection of signature genes from a test individual, wherein the collection of signature genes comprises at least two genes selected from the group consisting of GI—2094528, KIP2, NRG1, NBL1, Prostein, CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B, and PROK1; (b) deriving a score that captures the expression levels for the collection of signature genes; (c) providing a model comprising information correlating the score with prostate cancer relapse; and (d) comparing the score to the reference model, thereby determining the probability of prostate cancer relapse for the individual.
While the present invention is disclosed and exemplified with the 21 signature genes set forth above and further in the context of correlation to Gleason score in prostate cancer, the methods are universally applicable to the diagnosis and prognosis of a broad range of cancers and other conditions. The skilled person apprised of the invention disclosed herein will appreciate that any known predictor of disease extent for any condition can be selected to establish a GEX score for prognosis of relapse that can be more accurate or sensitive than relapse prediction solely based on the known predictor alone.
Accordingly, the invention provides a method for preparing a model for prognosis of an individual having a disease or condition. The method can include the steps of (a) obtaining from different individuals a plurality of tissue samples suspected of having a disease or condition, wherein the clinical outcome corresponding to each of the tissue samples is known, wherein a prognostic score of the tissue samples is known wherein the prognostic score includes stratified grades corresponding to the clinical outcome; (b) selecting a set of signature genes having an expression pattern that correlates positively or negatively in a statistically significant manner with the prognostic score; (c) independently deriving a prediction score for each signature gene in the plurality of tissue samples, wherein the prediction score correlates gene expression of each individual signature gene with the prognostic score; (d) deriving a gene expression (GEX) score based on a combination of the independently derived prediction scores in the plurality of tissue samples, wherein the GEX score correlates gene expression of the set of signature genes with the prognostic score; and (f) correlating the GEX score with the clinical outcome for each of the tissue samples, thereby establishing a model for prognosis of an individual having the disease or condition, wherein the model provides a higher resolution correlation with the clinical outcome than the strata of the prognostic score.
Individuals suspected of having any of a variety of diseases or conditions, such as cancer, can be evaluated using a method of the invention. Exemplary cancers that can be evaluated using a method of the invention include, but are not limited to hematoporetic neoplasms, Adult T-cell leukemia/lymphoma, Lymphoid Neoplasms, Anaplastic large cell lymphoma, Myeloid Neoplasms, Histiocytoses, Hodgkin Diseases (HD), Precursor B lymphoblastic leukemia/lymphoma (ALL), Acute myclogenous leukemia (AML), Precursor T lymphoblastic leukemia/lymphoma (ALL), Myclodysplastic syndromes, Chronic Mycloproliferative disorders, Chronic lymphocytic leukemia/small lymphocytic lymphoma (SLL), Chronic Myclogenous Leukemia (CML), Lymphoplasmacytic lymphoma, Polycythemia Vera, Mantle cell lymphoma, Essential Thrombocytosis, Follicular lymphoma, Myelofibrosis with Myeloid Metaplasia, Marginal zone lymphoma, Hairy cell leukemia, Hemangioma, Plasmacytoma/plasma cell myeloma, Lymphangioma, Glomangioma, Diffuse large B-cell lymphoma, Kaposi Sarcoma, Hemanioendothelioma, Burkitt lymphoma, Angiosarcoma, T-cell chronic lymphocytic leukemia, Hemangiopericytoma, Large granular lymphocytic leukemia, head & neck cancers, Basal Cell Carcinoma, Mycosis fungoids and sezary syndrome, Squamous Cell Carcinoma, Ceruminoma, Peripheral T-cell lymphoma, Osteoma, Nonchromaffin Paraganglioma, Angioimmunoblastic T-cell lymphoma, Acoustic Neurinoma, Adenoid Cystic Carcinoma, Angiocentric lymphoma, Mucoepidermoid Carcinoma, NK/T-cell lymphoma, Malignant Mixed Tumors, Intestinal T-cell lymphoma, Adenocarcinoma, Malignant Mesothelioma, Fibrosarcoma, Sarcomotoid Type lung cacer, Osteosarcoma, Epithelial Type lung cancer, Chondrosarcoma, Melanoma, cancer of the gastrointestinal tract, olfactory Neuroblastoma, Squamous Cell Carcinoma, Isolated Plasmocytoma, Adenocarcinoma, Inverted Papillomas, Carcinoid, Undifferentiated Carcinoma, Malignant Melanoma, Mucoepidermoid Carcinoma, Adenocarcinoma, Acinic Cell Carcinoma, Gastric Carcinoma, Malignant Mixed Tumor, Gastric Lymphoma, Gastric Stromal Cell Tumors, Amenoblastoma, Lymphoma, Odontoma, Intestinal Stromal Cell tumors, thymus cancers, Malignant Thymoma, Carcinids, Type I (Invasive thymoma), Malignant Mesethelioma, Type II (Thymic carcinoma), Non-mucin producing adenocarcinoma, Squamous cell carcinoma, Lymph epithelioma, cancers of the liver and biliary tract, Squamous Cell Carcinoma, Hepatocellular Carcinoma, Adenocarcinoma, Cholangiocarcinoma, Hepatoblastoma, papillary cancer, Angiosarcoma, solid Bronchioalveolar cancer, Fibrolameller Carcinoma, Small Cell Carcinoma, Carcinoma of the Gallbladder, Intermediate Cell carcinaoma, Large Cell Carcinoma, Squamous Cell Carcinoma, Undifferentiated cancer, cancer of the pancreas, cancer of the female genital tract, Squamous Cell Carcinoma, Cystadenocarcinoma, Basal Cell Carcinoma, Insulinoma, Melanoma, Gastrinoma, Fibrosarcoma, Glucagonamoa, Intaepithelial Carcinoma, Adenocarcinoma Embryonal, cancer of the kidney, Rhabdomysarcoma, Renal Cell Carcinoma, Large Cell Carcinoma, Nephroblastoma (Wilm's tumor), Neuroendocrine or Oat Cell carcinoma, cancer of the lower urinary tract, Adenosquamous Carcinoma, Urothelial Tumors, Undifferentiated Carcinoma, Squamous Cell Carcinoma, Carcinoma of the female genital tract, Mixed Carcinoma, Adenoacanthoma, Sarcoma, Small Cell Carcinoma, Carcinosarcoma, Leiomyosarcoma, Endometrial Stromal Sarcoma, cancer of the male genital tract, Serous Cystadenocarcinoma, Mucinous Cystadenocarcinoma, Sarcinoma, Endometrioid Tumors, Speretocytic Sarcinoma, Embyonal Carcinoma, Celioblastoma, Choriocarcinoma, Teratoma, Clear Cell Carcinoma, Leydig Cell Tumor, Unclassified Carcinoma, Sertoli Cell Tumor, Granulosa-Theca Cell Tumor, Sertoli-Leydig Cell Tumor, Disgerminoma, Undifferentiated Prostatic Carcinoma, Teratoma, Ductal Transitional carcinoma, breast cancer, Phyllodes Tumor, cancer of the bones joints and soft tissue, Paget's Disease, Multiple Myeloma, Insitu Carcinoma, Malignant Lymphoma, Invasive Carcinoma, Chondrosacrcoma, Mesenchymal Chondrosarcoma, cancer of the endocrine system, Osteosarcoma, Adenoma, Ewing Tumor, endocrine Carcinoma, Malignant Giant Cell Tumor, Meningnoma, Adamantinoma, Cramiopharlingioma, Malignant Fibrous Histiocytoma, Papillary Carcinoma, Histiocytoma, Follicular Carcinoma, Desmoplastic Fibroma, Medullary Carcinoma, Fibrosarcoma, Anoplastic Carcinoma, Chordoma, Adenoma, Hemangioendothelioma, Memangispericytoma, Pheochromocytoma, Liposarcoma, Neuroblastoma, Paraganglioma, Histiocytoma, Pineal cancer, Rhabdomysarcoms, Pineoblastoma, Leiomyosarcoma, Pineocytoma, Angiosarcoma, skin cancer, cancer of the nervous system, Melanoma, Schwannoma, Squamous cell carcinoma, Neurofibroma, Basal cell carcinoma, Malignant Periferal Nerve Sheath Tumor, Merkel cell carcinoma, Sheath Tumor, Extramamary Paget's Disease, Astrocytoma, Paget's Disease of the nipple, Fibrillary Astrocytoma, Glioblastoma Multiforme, Brain Stem Glioma, Cutaneous T-cell lymphoma, Pilocytic Astrocytoma, Xanthorstrocytoma, Histiocytosis, Oligodendroglioma, Ependymoma, Gangliocytoma, Cerebral Neuroblastoma, Central Neurocytoma, Dysembryoplastic Neuroepithelial Tumor Medulloblastoma, Malignant Meningioma, Primary Brain Lymphoma, Primary Brain Germ Cell Tumor, cancers of the eye, Squamous Cell Carcinoma, Mucoepidermoid Carcinoma, Melanoma, Retinoblastoma, Glioma, Meningioma, cancer of the heart, Myxoma, Fibroma, Lipoma, Papillary Fibroelastoma, Rhasdoyoma, or Angiosarcoma among others.
A prognostic score that can be used in the invention includes for example the Gleason score having stratified grades 1-9 that correspond to clinical outcome as set forth elsewhere herein. A further example of a prognostic score that is useful in the invention is cancer staging having stratified grades of stages 1, 2, 3 and 4. The invention can be used to provide a higher resolution correlation with the clinical outcome than the strata of the Gleason or cancer staging prognostic scores. Diseases or conditions other than cancer for which stratified grades have been correlated with clinical outcome can also be used in a method of the invention to determine a prognostic model or to determine a prognosis for an individual suspected of having the disease or condition. Exemplary clinical outcomes that can be determined from a model of the invention include, for example, relapse probability, survival rate, or time to relapse. Another clinical outcome that can be determined from a model of the invention is response to a particular course of therapy such as surgical removal of a tumor, radiation, or chemotherapy.
Any signature gene or combination of signature genes listed within Table 2 or Table 4 can be used in the methods, compositions, and kits of the present invention. Similarly, any additional gene known or discovered to be differentially expressed and correlated with Gleason score can be used in combination with some or all of the signature genes set forth within Table 2 or Table 4 and used in the methods, compositions, and kits of the present invention. In general, it is preferable to use signature genes for which the difference between the level of expression of the signature gene in prostate cancer cells or prostate-associated body fluids and the level of expression of the same signature gene in normal prostate cells or prostate-associated body fluids is as great as possible. Although the difference can be as small as the limit of detection of the method for assessing expression of the signature gene, it is preferred that the difference be at least greater than the standard error of the assessment method, and preferably a difference of at least 1.1-, 1.2-, 1.3-, 1.4-, 1.5-, 1.6-, 1.7-, 1.8-, 1.9-, 2-, 3-, 4-, 5-, 6-, 7-, 8-, 9-, 10-, 15-, 20-, 25-, 100-, 500-, 1000-fold or greater. It also is preferable to use signature genes for which the correlation with Gleason score is more rather than less significant.
The skilled person will appreciate that patient tissue samples containing prostate cells or prostate cancer cells may be used in the methods of the present invention including, but not limited to those aimed at predicting relapse probability. In these embodiments, the level of expression of the signature gene can be assessed by assessing the amount, e.g. absolute amount or concentration, of a signature gene product, e.g., protein and RNA transcript encoded by the signature gene and fragments of the protein and RNA transcript) in a sample, e.g., stool and/or blood obtained from a patient. The sample can, of course, be subjected to a variety of well-known post-collection preparative and storage techniques (e.g. fixation, storage, freezing, lysis, homogenization, DNA or RNA extraction, ultrafiltration, concentration, evaporation, centrifugation, etc.) prior to assessing the amount of the signature gene product in the sample.
In the methods of the invention aimed at preparing a model for prostate cancer relapse prediction, it is understood that the particular clinical outcome associated with each sample contributing to the model must be known. Consequently, the model can be established using archived tissues. In the methods of the invention aimed at preparing a model for prostate cancer relapse prediction, total RNA is generally extracted from the source material of interest, generally an archived tissue such as a formalin-fixed, paraffin-embedded tissue, and subsequently purified. Methods for obtaining robust and reproducible gene expression patterns from archived tissues, including formalin-fixed, paraffin-embedded (FFPE) tissues are taught in United States Patent Publication 2004/0259105, which is incorporated herein by reference in its entirety. Commercial kits and protocols for RNA extraction from FFPE tissues are available including, for example, ROCHE High Pure RNA Paraffin Kit (Roche) MasterPureTM Complete DNA and RNA Purification Kit (EPICENTRE®Madison, Wis.); Paraffin Block RNA Isolation Kit (Ambion, Inc.) and RNeasyTM Mini kit (Qiagen, Chatsworth, Calif.).
The use of FFPE tissues as a source of RNA for RT-PCR has been described previously (Stanta et al., Biotechniques 11:304-308 (1991); Stanta et al., Methods Mol. Biol. 86:23-26 (1998); Jackson et al., Lancet 1:1391 (1989); Jackson et al., J. Clin. Pathol. 43:499-504 (1999); Finke et al., Biotechniques 14:448-453 (1993); Goldsworthy et al., Mol. Carcinog. 25:86-91 (1999); Stanta and Bonin, Biotechniques 24:271-276 (1998); Godfrey et al., J. Mol. Diagnostics 2:84 (2000); Specht et al., J. Mol. Med. 78:B27 (2000); Specht et al., Am. J. Pathol. 158:419-429 (2001)). For quick analysis of the RNA quality, RT-PCR can be performed utilizing a pair of primers targeting a short fragment in a highly expressed gene, for example, actin, ubiquitin, gapdh or other well-described commonly used housekeeping gene. If the cDNA synthesized from the RNA sample can be amplified using this pair of primers, then the sample is suitable for the a quantitative measurements of RNA target sequences by any method preferred, for example, the DASL assay, which requires only a short cDNA fragment for the annealing of query oligonucleotides.
There are numerous tissue banks and collections including exhaustive samples from all stages of a wide variety of disease states, most notably cancer. The ability to perform genotyping and/or gene expression analysis, including both qualitative and quantitative analysis on these samples enables the application of this methodology to the methods of the invention. In particular, the ability to establish a correlation of gene expression and a known predictor of disease extent and/or outcome by probing the genetic state of tissue samples for which clinical outcome is already known, allows for the establishment of a correlation between a particular molecular signature and the known predictor, such as a Gleason score, to derive a GEX score that allows for a more sensitive prognosis than that based on the known predictor alone. The skilled person will appreciate that by building databases of molecular signatures from tissue samples of known outcomes, many such correlations can be established, thus allowing both diagnosis and prognosis of any condition.
Tissue samples useful for preparing a model for prostate cancer relapse prediction include, for example, paraffin and polymer embedded samples, ethanol embedded samples and/or formalin and formaldehyde embedded tissues, although any suitable sample may be used. In general, nucleic acids isolated from archived samples can be highly degraded and the quality of nucleic preparation can depend on several factors, including the sample shelf life, fixation technique and isolation method. However, using the methodologies taught in United States Patent Publication 2004/0259105, which have the significant advantage that short or degraded targets can be used for analysis as long as the sequence is long enough to hybridize with the oligonucleotide probes, highly reproducible results can be obtained that closely mimic results found in fresh samples.
Archived tissue samples, which can be used for all methods of the invention, typically have been obtained from a source and preserved. Preferred methods of preservation include, but are not limited to paraffin embedding, ethanol fixation and formalin, including formaldehyde and other derivatives, fixation as are known in the art. A tissue sample may be temporally “old”, e.g. months or years old, or recently fixed. For example, post-surgical procedures generally include a fixation step on excised tissue for histological analysis. In a preferred embodiment, the tissue sample is a diseased tissue sample, particularly a prostate cancer tissue, including primary and secondary tumor tissues as well as lymph node tissue and metastatic tissue.
Thus, an archived sample can be heterogeneous and encompass more than one cell or tissue type, for example, tumor and non-tumor tissue. Preferred tissue samples include solid tumor samples including, but not limited to, tumors of the prostate. It is understood that in applications of the present invention to conditions other than prostate cancer the tumor source can be brain, bone, heart, breast, ovaries, prostate, uterus, spleen, pancreas, liver, kidneys, bladder, stomach and muscle. Similarly, depending on the condition, suitable tissue samples include, but are not limited to, bodily fluids (including, but not limited to, blood, urine, serum, lymph, saliva, anal and vaginal secretions, perspiration and semen, of virtually any organism, with mammalian samples being preferred and human samples being particularly preferred). In embodiments directed to methods of establishing a model for relapse prediction, the tissue sample is one for which patient history and outcome is known. Generally, the invention methods can be practiced with the signature gene sequence contained in an archived sample or can be practiced with signature gene sequences that have been physically separated from the sample prior to performing a method of the invention.
If required, a nucleic acid sample having the signature gene sequence(s) are prepared using known techniques. For example, the sample can be treated to lyse the cells, using known lysis buffers, sonication, electroporation, etc., with purification and amplification as outlined below occurring as needed, as will be appreciated by those in the art. In addition, the reactions can be accomplished in a variety of ways, as will be appreciated by those in the art. Components of the reaction may be added simultaneously, or sequentially, in any order, with preferred embodiments outlined below. In addition, the reaction can include a variety of other reagents which can be useful in the assays. These include reagents like salts, buffers, neutral proteins, e.g. albumin, detergents, etc., which may be used to facilitate optimal hybridization and detection, and/or reduce non-specific or background interactions. Also reagents that otherwise improve the efficiency of the assay, such as protease inhibitors, nuclease inhibitors, anti-microbial agents, etc., can be used, depending on the sample preparation methods and purity.
In a preferred embodiment mRNA is isolated from paraffin embedded samples as is known in the art. Preferred methods include the use of the Paraffin Block RNA Isolation Kit by Ambion (Catalog number 1902, which instruction manual is incorporated herein by reference) or the high pure RNA parafin kit by Roche (cat #3270289). Samples of mRNA can be obtained from other samples using methods known in the art including for example, those described in Sambrook et al., Molecular Cloning: A Laboratory Manual, 3rd edition, Cold Spring Harbor Laboratory, New York (2001) or in Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1998), or those that are commercially available such as the Invitrogen PureLink miRNA isolation kit (cat# K1570) or mRNA isolation kits from Ambion (Austin, Tex.). Once prepared, mRNA or other nucleic acids are analyzed by methods known to those of skill in the art. The nucleic acid sequence corresponding to a signature gene can be any length, with the understanding that longer sequences are more specific. Recently developed methods for obtaining robust and reproducible gene expression patterns from archived tissues, including formalin-fixed, paraffin-embedded (FFPE) tissues as taught in United States Patent Application Publication No. 2004/0259105 have the significant advantage that short or degraded targets can be used for analysis as long as the sequence is long enough to hybridize with the oligonucleotide probes. Thus, even degraded target nucleic acids can be analyzed. Preferably a nucleic acid corresponding to a signature gene is at least 20 nucleotides in length. Preferred ranges are from 20 to 100 nucleotides in length, with from 30 to 60 nucleotides being more preferred and from 40 to 50 being most preferred.
In addition, when nucleic acids are to be detected preferred methods utilize cutting or shearing techniques to cut the nucleic acid sample containing the target sequence into a size that will facilitate handling and hybridization to the target. This can be accomplished by shearing the nucleic acid through mechanical forces (e.g. sonication) or by cleaving the nucleic acid using restriction endonucleases, or any other methods known in the art. However, in most cases, the natural degradation that occurs during archiving results in “short” oligonucleotides. In general, the methods of the invention can be done on oligonucleotides as short as 20-100 basepairs, with from 20 to 50 being preferred, and between 40 and 50, including 44, 45, 46, 47, 48 and 49 being the most preferred.
Tissue samples useful in a method of the invention for deriving a prostate cancer gene expression score or in a method of the invention for predicting the probability of relapse of prostate cancer in an individual, include the tissue samples described above as useful for preparing a model for prostate cancer relapse prediction, but also include fresh and non-archived samples. Unlike for tissue samples useful for preparing a model for prostate cancer relapse prediction, the tissues used for deriving a prostate cancer GEX score or in a method of the invention for predicting the probability of relapse of prostate cancer in an individual, for obvious reasons, do not have the requirement that clinical outcome be known. Consequently, freshly obtained tissue samples can also be used in the individual methods for GEX score determination and relapse prediction methods, such as in a prospective study or clinical trial.
The methods of the invention depend on the detection of differentially expressed genes for expression profiling across heterogeneous tissues. Thus, the methods depend on profiling genes whose expression in certain tissues is activated to a higher or lower level in an individual afflicted with a condition, for example, cancer, such as prostate cancer, relative to its expression in non-cancerous tissues or in a control subject. Gene expression can be activated to a higher or lower level at different stages of the same conditions and a differentially expressed gene can be either activated or inhibited at the nucleic acid level or protein level, or may be subject to alternative splicing to result in a different polypeptide product. Such differences can be evidenced by a change in mRNA levels, surface expression, secretion or other partitioning of a polypeptide, for example. For the purpose of this invention, differential gene expression is considered to be present when there is at least about 1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, to two-fold, preferably at least about four-fold, more preferably at least about six-fold, most preferably at least about ten-fold difference between the expression of a given gene in normal and diseased tissues.
Differential signature gene expression can be identified, or confirmed using methods known in the art such as quantitative RT-PCR. In particular embodiments, differential signature gene expression can be identified, or confirmed using microarray techniques. Thus, the signature genes can be measured in either fresh or paraffin-embedded tumor tissue, using microarray technology. In this method, polynucleotide sequences of interest are plated, or arrayed, on a microchip substrate. The arrayed sequences are then hybridized with specific DNA probes from cells or tissues of interest. In a preferred embodiment the technology combines fiber optic bundles and beads that self-assemble into an array. Each fiber optic bundle contains thousands to millions of individual fibers depending on the diameter of the bundle. Sensors are affixed to each bead in a given batch. The particular molecules on a bead define that bead's function as a sensor. To form an array, fiber optic bundles are dipped into pools of coated beads. The coated beads are drawn into the wells, one bead per well, on the end of each fiber in the bundle. The present invention is not limited to the solid supports described above. Indeed, a variety of other solid supports are contemplated including, but not limited to, glass microscope slides, glass wafers, gold, silicon, microchips, and other plastic, metal, ceramic, or biological surfaces. Microarray analysis can be performed by commercially available equipment, following manufacturer's protocols, such as by using Illumina's technology.
Exemplary arrays that are useful include, without limitation, a Sentrix® Array or Sentrix® BeadChip Array available from Illumina®, Inc. (San Diego, Calif.) or others including beads in wells such as those described in U.S. Pat. Nos. 6,266,459, 6,355,431, 6,770,441, and 6,859,570; and PCT Publication No. WO 00/63437, each of which is hereby incorporated by reference. Other arrays having particles on a surface include those set forth in US 2005/0227252; US 2006/0023310; US 2006/006327; US 2006/0071075; US 2006/0119913; U.S. Pat. No. 6,489,606; U.S. Pat. No. 7,106,513; U.S. Pat. No. 7,126,755; U.S. Pat. No. 7,164,533; WO 05/033681; and WO 04/024328, each of which is hereby incorporated by reference.
An array of beads useful in the invention can also be in a fluid format such as a fluid stream of a flow cytometer or similar device. Exemplary formats that can be used in the invention to distinguish beads in a fluid sample using microfluidic devices are described, for example, in U.S. Pat. No. 6,524,793. Commercially available fluid formats for distinguishing beads include, for example, those used in XMAPTM technologies from Luminex or MPSSTM methods from Lynx Therapeutics.
Further examples of commercially available microarrays that can be used in the invention include, for example, an Affymetrix® GeneChip® microarray or other microarray synthesized in accordance with techniques sometimes referred to as VLSIPSTM (Very Large Scale Immobilized Polymer Synthesis) technologies as described, for example, in U.S. Pat. Nos. 5,324,633; 5,744,305; 5,451,683; 5,482,867; 5,491,074; 5,624,711; 5,795,716; 5,831,070; 5,856,101; 5,858,659; 5,874,219; 5,968,740; 5,974,164; 5,981,185; 5,981,956; 6,025,601; 6,033,860; 6,090,555; 6,136,269; 6,022,963; 6,083,697; 6,291,183; 6,309,831; 6,416,949; 6,428,752 and 6,482,591, each of which is hereby incorporated by reference.
A spotted microarray can also be used in a method of the invention. An exemplary spotted microarray is a CodeLinkTM Array available from Amersham Biosciences. Another microarray that is useful in the invention is one that is manufactured using inkjet printing methods such as SurePrintTM Technology available from Agilent Technologies. Other microarrays that can be used in the invention include, without limitation, those described in Butte, Nature Reviews Drug Discov. 1:951-60 (2002) or U.S. Pat. Nos. 5,429,807; 5,436,327; 5,561,071; 5,583,211; 5,658,734; 5,837,858; 5,919,523; 6,287,768; 6,287,776; 6,288,220; 6,297,006; 6,291,193; and 6,514,751; and WO 93/17126; WO 95/35505, each of which is hereby incorporated by reference.
DASL can be used for quantitative measurements of RNA target sequences as well as for DNA target sequences. DASL is described, for example, in Fan et al., Genome Res. 14:878-85 (2004); US 2003/0108900 and US 2004/0259105, each of which is incorporated herein by reference. Notably, the sensitivity of DASL using RNA from paraffin samples is about 80% compared to the assay using RNA prepared from fresh frozen samples, with results up to 90% sensitivity observed. Gene expression can be monitored and compared in formalin-fixed, paraffin-embedded clinical samples archived for more than 5 years.
The expression patterns for signature genes are determined based on quantitative detection of nucleic acids or oligonucleotides corresponding to the signature genes, which means at least two nucleotides covalently linked together. Thus, the invention also provides a collection of nucleic acids and oligonucleotides that correspond to a signature gene or a set of signature genes. A nucleic acid useful in the methods of the invention will generally contain phosphodiester bonds, although in some cases, nucleic acid analogs are included that may have alternate backbones, including, for example, phosphoramide (Beaucage et al., Tetrahedron 49(10):1925 (1993) and references therein; Letsinger, J. Org. Chem. 35:3800 (1970); Sprinzl et al., Eur. J. Biochem. 81:579 (1977); Letsinger et al., Nucl. Acids Res. 14:3487 (1986); Sawai et al, Chem. Lett. 805 (1984), Letsinger et al., J. Am. Chem. Soc. 110:4470 (1988); and Pauwels et al., Chemica Scripta 26:141 91986)), phosphorothioate (Mag et al., Nucleic Acids Res. 19:1437 (1991); and U.S. Pat. No. 5,644,048), phosphorodithioate (Briu et al., J. Am. Chem. Soc. 111:2321 (1989), O-methylphophoroamidite linkages (see Eckstein, Oligonucleotides and Analogues: A Practical Approach, Oxford University Press), and peptide nucleic acid backbones and linkages (see Egholm, J. Am. Chem. Soc. 114:1895 (1992); Meier et al., Chem. Int. Ed. Engl. 31:1008 (1992); Nielsen, Nature, 365:566 (1993); Carlsson et al., Nature 380:207 (1996), all of which are incorporated by reference). Other analog nucleic acids include those with positive backbones (Denpcy et al., Proc. Natl. Acad. Sci. USA 92:6097 (1995); non-ionic backbones (U.S. Pat. Nos. 5,386,023, 5,637,684, 5,602,240, 5,216,141 and 4,469,863; Kiedrowshi et al., Angew. Chem. Intl. Ed. English 30:423 (1991); Letsinger et al., J. Am. Chem. Soc. 110:4470 (1988); Letsinger et al., Nucleoside & Nucleotide 13:1597 (1994); Chapters 2 and 3, ASC Symposium Series 580, “Carbohydrate Modifications in Antisense Research”, Ed. Y. S. Sanghui and P. Dan Cook; Mesmaeker et al., Bioorganic & Medicinal Chem. Lett. 4:395 (1994); Jeffs et al., J. Biomolecular NMR 34:17 (1994); Tetrahedron Lett. 37:743 (1996)) and non-ribose backbones, including those described in U.S. Pat. Nos. 5,235,033 and 5,034,506, and Chapters 6 and 7, ASC Symposium Series 580, “Carbohydrate Modifications in Antisense Research”, Ed. Y. S. Sanghui and P. Dan Cook. Nucleic acids containing one or more carbocyclic sugars are also included within the definition of nucleic acids (see Jenkins et al., Chem. Soc. Rev. (1995) pp 169-176). Several nucleic acid analogs are described in Rawls, C & E News Jun. 2, 1997 page 35. Modifications of the ribose-phosphate backbone may be done to facilitate the addition of labels, or to increase the stability and half-life of such molecules in physiological environments. Nucleic acid analogs can find use in the methods of the invention as well as mixtures of naturally occurring nucleic acids and analogs.
The nucleic acids corresponding to signature genes can be single stranded or double stranded, as specified, or contain portions of both double stranded or single stranded sequence. The nucleic acid can be DNA, both genomic and cDNA, RNA or a hybrid, where the nucleic acid contains any combination of deoxyribo- and ribo-nucleotides, and any combination of bases, including, for example, uracil, adenine, thymine, cytosine, guanine, inosine, xanthine hypoxanthine, isocytosine, isoguanine A nucleic acid sequence corresponding to a signature gene can be a portion of the gene, a regulatory sequence, genomic DNA, cDNA, RNA including mRNA and rRNA, or others.
A nucleic acid sequence corresponding to a signature gene can be derived from the tissue sample, or from a secondary source such as a product of a reaction such as, for example, a detection sequence from an invasive cleavage reaction, a ligated probe from an OLA or DASL reaction, an extended probe from a PCR reaction, or PCR amplification product, (“amplicon”). Exemplary methods for preparing secondary probes from target sequences are described in US 2003/0108900; US 2003/0170684; US 2003/0215821; US 2004/0121364; and US 2005/0181394. Thus, a nucleic acid sequence corresponding to a signature gene can be derived from the primary or from a secondary source of nucleic acid.
As will be appreciated by those in the art, a complementary nucleic acid sequence useful in the methods of the invention can take many forms and probes are made to hybridize to nucleic acid sequences to determine the presence or absence of the signature gene in a sample. In a preferred embodiment, a plurality of nucleic acid sequences is detected. As used herein, “plurality” or grammatical equivalents herein refers to at least 2, 10, 20, 25, 50, 100 or 200 different nucleic sequences, while at least 500 different nucleic sequences is preferred. More preferred is at least 1000, with more than 5000 or 10,000 particularly preferred and more than 50,000 or 100,000 most preferred. Detection can be performed on a variety of platforms such as those set forth above or in the Examples.
The expression level of a signature gene in a tissue sample can be determined by contacting nucleic acid molecules derived from the tissue sample with a set of probes under conditions where perfectly complementary probes form a hybridization complex with the nucleic acid sequences corresponding to the signature genes, each of the probes including at least two universal priming sites and a signature gene target-specific sequence; amplifying the probes forming the hybridization complexes to produce amplicons; and detecting the amplicons, wherein the detection of the amplicons indicates the presence of the nucleic acid sequences corresponding to the signature gene in the tissue sample; and determining the expression level of the signature gene.
In the context of the present invention, multiplexing refers to the detection, analysis or amplification of a plurality of nucleic acid sequences corresponding to the signature genes. In one embodiment multiplex refers to the number of nucleic acid sequences corresponding to a signature gene to be analyzed in a single reaction, vessel or step. The multiplexing method is useful for detection of a single nucleic acid sequence corresponding to a signature gene as well as a plurality of nucleic acid sequences corresponding to a set of signature genes. In addition, as described below, the methods of the invention can be performed simultaneously and in parallel in a large number of tissue samples.
The expression level of nucleic acid sequences corresponding to a set of signature genes in a tissue sample can be determined by contacting nucleic acid molecules derived from the tissue sample with a set of probes under conditions where complementary probes form a hybridization complex with the signature gene-specific nucleic acid sequences, each of the probes including at least two universal priming sites and a signature gene-specific nucleic acid sequence; amplifying the probes forming the hybridization complexes to produce amplicons; detecting the amplicons, wherein the detection of the amplicons indicates the presence of the nucleic acid sequences corresponding to the set of signature genes in the tissue sample; and determining the expression level of the target sequences, wherein the expression of at least two, at least three, at least five signature gene-specific sequences is detected.
The presence of one, two or a plurality of nucleic acid sequences corresponding to a set of signature genes can be determined in a tissue sample using single, double or multiple probe configurations. The methods of the invention can be practiced with tissue samples having substantially degraded nucleic acids. Although methods for pre-qualifying samples with respect to nucleic acid degradation are described above, those skilled in the art will recognize that other detection methods described herein or known in the art can be used to detect RNA levels in a sample suspected of having degraded nucleic acids, thereby determine the level of nucleic acid degradation in accordance with the invention.
The present invention particularly draws on methodologies outlined in US 2003/0215821; US 2004/0018491; US 2003/0036064; US 2003/0211489, each of which is expressly incorporated by reference in their entirety. In addition, universal priming methods are described in detail in US 2002/0006617; US 2002/0132241, each of which is expressly incorporated herein by reference. In addition, multiplex methods are described in detail US 2003/0211489; US 2003/0108900, each of which is expressly incorporated herein by reference. In general, the methods of the invention can be performed in a variety of ways, as further described below and in the cited applications incorporated by reference. For example, mRNA signature samples can initially be subjected to a “complexity reduction” step, whereby the presence of a particular target is confirmed by adding probes that are enzymatically modified in the presence of the signature gene-specific nucleic acid sequence. The modified probes are then amplified and detected in a wide variety of ways. Preferred embodiments draw on multiplexing methods, which allow for the simultaneous detection of a number of nucleic acid sequences, for example, corresponding to a set of signature genes, as well as multiplexing amplification reactions, for example by using universal priming sequences to do multiplex PCR reactions. If desired, the initial step also can be both a complexity reduction and an amplification step.
“Nucleic acid sequence” or grammatical equivalents herein referred to as corresponding to a signature gene means the order and type of nucleotides in a single strand of nucleic acid. The nucleic sequence can be a portion of a gene, a regulatory sequence, genomic DNA, cDNA, RNA including mRNA and rRNA, or others. A preferred embodiment utilizes mRNA as the primary target sequence. As is outlined herein, the nucleic acid sequence can be a sequence from a sample, or a secondary target such as, for example, a product of a reaction such as a detection sequence from an invasive cleavage reaction, a ligated probe from an OLA or DASL reaction, an extended probe from a PCR reaction, or PCR amplification product, (“amplicon”). A nucleic acid sequence corresponding to a signature gene can be any length, with the understanding that longer sequences are more specific. Probes are made to hybridize to nucleic acid sequences to determine the presence or absence of expression of a signature gene in a sample.
The invention also provides a collection of isolated probes specific for prostate cancer signature genes consisting essentially of probes specific for GI—2094528, KIP2, NRG1, NBL1, Prostein, CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B and PROK1. The invention also provides a collection of isolated probes specific for prostate cancer signature genes consisting of probes specific for GI—2094528, KIP2, NRG1, NBL1, Prostein, CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B and PROK1. The invention also provides a collection of isolated probes specific for prostate cancer signature genes comprising probes specific for GI—2094528, KIP2, NRG1, NBL1, Prostein, CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B and PROK1. Also provided is a collection of isolated probes specific for prostate cancer signature genes comprising probes specific for a subset of the collection consisting of GI—2094528, KIP2, NRG1, NBL1, Prostein, CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B and PROK1. Exemplary subsets include those set forth elsewhere herein.
Thus, the invention also provides a collection of isolated probes specific for prostate cancer signature genes including any subset of the 21 genes set forth in Table 5 including, for example, at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 of the 21 genes. The invention also provides a collection of isolated probes specific for prostate cancer signature genes including any subset of the set of genes consisting of MKI67, GI—2094528, HOXC6, CCK, memD, FBP1, and CDC6 including, for example, at least 2, 3, 4, 5 or 6 of the 7 genes.
A method of the invention can further include a step of producing a report identifying, for example, a reference model, a set of signature genes, a prediction score, a GEX score. The report can include data obtained from a method of the invention in a format that can be subsequently analyzed to identify a reference model, a set of signature genes, a prediction score, a GEX score. Thus, the invention further provides a report of at least one result obtained by a method of the invention. A report of the invention can be in any of a variety of recognizable formats including, for example, an electronic transmission, computer readable memory, an output to a computer graphical user interface, compact disk, magnetic disk or paper. Other formats suitable for communication between humans, machines or both can be used for a report of the invention. The methods of the invention can, in part, be conveniently performed on a computer apparatus. Performing one or more steps of an invention method on a computer apparatus is particularly useful when analyzing a large number of parameters such as a large number of tissue samples.
In one embodiment, the invention provides a diagnostic method of assessing whether a patient who has had prostate cancer has a higher than normal risk for recurrence of the prostate cancer or other cancer, including the steps of comparing the GEX score calculated by a method of the invention in a patient sample comparing it to a model for relapse prediction prepared by a method of the invention. A similar GEX score in the patient sample as compared to the model provides a more accurate relapse predictor than Gleason score alone.
In one embodiment, the invention provides a diagnostic method of assessing whether a patient has a higher than normal risk of having or developing a prostate cancer. Small samples, such as those obtained using LCM in needle biopsies, with or without tumor glands, can be used to assess outcomes prior to definitive therapy. This test can give information on diagnosis as well as prognosis through needle biopsy samples. Such a test provides a diagnostic test for routine clinical use.
The invention includes compositions, kits, and methods for assessing the probability of relapse of cancer for an individual from which a sample is obtained. The sample can be, for example, an archived tissue sample or a sample obtained from a patient. Where necessary, the compositions, kits, and methods are adapted for use with samples other than patient samples. For example, when the sample to be used is a parafinized, archived human tissue sample, it can be necessary to adjust the ratio of compounds in the compositions of the invention, in the kits of the invention, or the methods used to assess levels of gene expression in the sample. Such methods are well known in the art and within the skill of the ordinary artisan. A kit is any manufacture (e.g. a package or container) including at least one reagent, e.g. a probe, for specifically detecting the expression of a signature gene of the invention. The kit may be promoted, distributed, or sold as a unit for performing the methods of the present invention. It is recognized that the compositions, kits, and methods of the invention will be of particular utility to patients having a history of prostate cancer and their medical advisors.
The practice of the present invention employs, unless otherwise indicated, conventional techniques of molecular biology (including recombinant techniques), microbiology, cell biology, and biochemistry, which are within the skill of the art. Such techniques are explained in the literature, such as, “Molecular Cloning: A Laboratory Manual”, Second edition (Sambrook et al., 1989); “Oligonucleotide Synthesis” (M. J. Gait, ed., 1984); “Animal Cell Culture” (R. I. Freshney, ed., 1987); “Methods in Enzymology” (Academic Press, Inc.); “Handbook of Experimental Immunology”, Fourth edition (D. M. Weir & C. C. Blackwell, eds., Blackwell Science Inc., 1987); “Gene Transfer Vectors for Mammalian Cells” (J. M. Miller & M. P. Calos, eds., 1987); “Current Protocols in Molecular Biology” (F. M. Ausubel et al., eds., 1987); and “PCR: The Polymerase Chain Reaction”, (Mullis et al., eds., 1994).
Although the use of the 21 genes, and subsets thereof, has been exemplified with respect to prognosis and diagnosis methods utilizing expression levels of mRNA species produced by these genes, it will be understood that similar diagnostic and prognostic methods can utilize other measures such as methylation levels for the genes which can be correlated with expression levels or a measure of the level or activities of the protein products of the genes. Methylation can be determined using methods known in the art such as those set forth in U.S. Pat. No. 6,200,756 or US 2003/0170684, each of which is incorporated herein by reference. The level and activity of proteins can be determined using methods known in the art such as antibody detection techniques or enzymatic assays particular to the activity being evaluated. Furthermore, prognosis or diagnosis can be based on the presence of mutations or polymorphisms identified in the genes that affect expression of the gene or activity of the protein product.
It is understood that modifications which do not substantially affect the activity of the various embodiments of this invention are also included within the definition of the invention provided herein. Accordingly, the following examples are intended to illustrate but not limit the present invention.
EXAMPLE I
Correlation Between Gene Expression Signature and Gleason Score
This example shows the calculation of a Gene EXpression score (GEX), which is an expression analogy of Gleason score derived from 16 genes and which showed a better correlation (r=0.62) with Gleason score than correlation of any individual gene.
A candidate gene approach focused on a set of “informative” genes that are the most relevant to the subjects of this study was taken as has been described by (Lossos et al., N Engl J Med 350:1828-37 (2004); Paik et al., 2004; Ramaswamy et al., J Clin Oncol 20:1932-41, (2002); van de Vijver et al., N Engl J Med 347:1999-2009 (2002)). The genes were selected based on: (1) Biological relevance. These include tumor suppressor genes and oncogenes, genes that are indirectly involved in cancer development, for example, DNA repair genes; metastasis-inhibitor genes, genes regulated by various signaling pathways, and/or responsible for altered cell growth and differentiation, apoptosis; or genes considered to be targets for oncogenic transformation. (2) Publicly reported lists of genes differentially expressed in prostate cancer as described by (Bettuzzi et al., Cancer Res 63:3469-72 (2003); Dhanasekaran et al., Nature 412:822-6 (2001); Ernst et al. Am J Pathol 160:2169-80 (2002); Febbo and Sellers, J Urol 170:S11-9; discussion S19-20 (2003); Glinsky et al., J Clin Invest 113:913-23 (2004); Henshall et al., Cancer Res 63:4196-203 (2003); Lapointe et al., Proc Natl Acad Sci USA 101:811-6 (2004); Latil et al., Clin Cancer Res 9:5477-85 (2003); Luo et al., Prostate 51:189-200 (2002); Nelson et al., N Engl J Med 349:366-81 (2003); Ramaswamy et al., Nat Genet 33:49-54 (2003); Singh et al., Cancer Cell 1:203-9 (2002); Stamey et al., J Urol 166:2171-7, (2001); Stuart et al., Proc Natl Acad Sci USA 101:615-20 (2004); van 't Veer et al., Nature 415:530-6 (2002); Welsh et al., Cancer Res 61:5974-8 (2001). As set forth in Table 3, a list of 512 genes was selected from these gene lists based on their overlapping occurrences among the studies, differential expression levels and biological relevance. In addition, 20 negative controls were included, designed to target sequences which are not present in the human genome and used to assess assay specificity.
The RNA samples assayed in this study were extracted from FFPE tissues. 200 ng of total RNA isolated from each FFPE tissue block was converted into cDNA, and two independent DASL assays were performed for each RNA sample as described by (Fan et al., Genome Res. 14:878-85 (2004)).
Briefly, surgically removed specimens (radical prostatectomy specimens) were processed under routine pathological protocol, and examined by at least two pathologists. A study number was assigned to the specimen and the patient identification information (names and hospital identification number) was also recorded at the time of specimen retrieval. This data were stored in a Microsoft Excel and Access database. The specimens usually were received in the pathology laboratory fresh within 45 minutes of removal. Each specimen was fixed in 10% buffered formalin overnight.
Representative sections were submitted for tissue processing and paraffin embedding. 5-gm thick sections were made for routine Hamatoxylin and eosin stains. Specific tissue blocks that included areas of carcinoma were selected for RNA extraction. RNA was procured from FFPE cancer tissue and nearby non-cancerous tissue. For each pathologic tissue, the percentage of tumor content was estimated and used as a reference for gene expression pattern analysis. RNA was extracted from four to five 5-μm sections using an RNA extraction kit (Roche High Pure RNA Paraffin kit), yielding 0.5-3 μg of total RNA.
A total of 71 tissue samples were entered into this study (Table 1). This consists of 29 cases of prostate carcinomas of low risk group patients, 26 cases of carcinomas of intermediate risk group, 16 cases of carcinomas of high risk group. Low risk group patients had a serum PSA ≦10 ng/ml, Gleason summary score ≦6 and a digital rectal examination (DRE) of T1c/T2a. Intermediate risk group patients had a serum PSA 10-20 ng/ml, Gleason summary score of 7 and DRE T2b/T2c. The high risk group patients had a serum PSA >20 ng/ml, Gleason summary score of 8-10 and DRE T3a/T3b. All tumor blocks contained at least 10% of malignant glands. In addition, 34 matched, non-tumor prostate tissues were used as controls. These tissues were various compositions of inflammation, stroma, benign glandular hyperplasia, and glandular atrophy.
Data regarding tissue samples were initially stored in a Microsoft Access file detailing the location, specimen number, and pathologic diagnosis. Approval was obtained from the UCSD IRB (#040487X) to study patient's existing tissue materials and review of pertinent medical records. The clinical information was de-identified from the original patient identification prior to data analysis so the findings will not be possible to trace back to the original patient.
To identify genes that are prognostically significant, patient history was provided for clinical correlation. Review of clinical data included demographic, clinical and laboratory data that is available either at the time of specimen collection (cross-sectional data) or becomes available at a later time point (longitudinal data). Data obtained from the patient treatment file (PTF), outpatient clinic file (OPC), and Computerized Patient Record System (CPRS), including lab, Systematized Nomenclature of Medicine (SNOMED), and tumor registry data. Information included 6-84 months follow up on the study patients and control subjects. Information relevant to the patient's diagnosis were obtained (Table 1), which include, but are not limited to, age, ethnicity, serum PSA at the time of surgery, tumor localization, pertinent past medical history related to co-morbidity, other oncological history, family history for cancer, physical exam findings, radiological findings, biopsy date, biopsy result, types of operation performed (radical retropubic or radical perineal prostatectomy), TNM staging, neoadjuvant therapy (i.e. chemotherapy, hormones), adjuvant or salvage radiotherapy, hormonal therapy for a rising PSA (biochemical disease relapse), local vs. distant disease recurrence and survival outcome.







TABLE 1





Patient Demographics.



















Mean Age
68.9
(55-81)



Mean PSA
8.1
(1.76-24.03)



Months Follow Up
43.9 ± 15
(6-84)















Numbers







Biopsy Risk Group



Low
29



Intermediate
26



High
16



Gleason Grade Distribution



5
2



6
8



7
31



8
26



9
3



Relapse



No
55



Yes
16



Survival



Alive
60



Dead
11



AJCC TNM Stage



I
0



II
53



III
15



IV
3










To assess their integrity, the RNA samples were measured on a Bioanalyzer (FIG. 7). In addition, aliquots of the cDNA reactions were taken for a real-time PCR analysis of a highly expressed housekeeping gene (RPL13A). Highly reproducible gene expression profiles were obtained for the replicates of each FFPE sample (R2=0.99), even though a wide range of RNA degradation was detected in these samples that had up to 8 cycle difference in qPCR (i.e.  ̃170-fold difference in “PCR-able” RNA input) for the RPL13A gene (FIG. 6). Under the conditions used, it was determined that a reasonable expectation of reliable data in the DASL assay was assured if samples did not exhibit a Ct of more than 28 cycles. In addition, similar expression profiles were obtained with RNAs extracted independently from separate cuts of the same paraffin tissue blocks (R2=0.93) (data not shown).
The randomly ordered BeadArrayTM technology (Michael et al., Anal Chem 70, 1242-8 (1998); Walt, Science 287, 451-2 (2000)) has been developed at Illumina as a platform for SNP genotyping (Fan et al., Cold Spring Harb Symp Quant Biol 68:69-78 (2003); Gunderson et al., Nat Genet 37:549-54 (2005)), gene expression profiling (Bibikova et al. Am J Pathol 165:1799-807 (2004); Fan et al., Genome Res 14:878-85 (2004); Kuhn et al., Genome Res 14:2347-56 (2004); Yeakley et al., Nat Biotechnol 20:353-8 (2002)) and DNA methylation detection (Bibikova et al., Genome Res 16:383-93 (2006)). Each array was assembled on an optical fiber bundle consisting of about 50,000 individual fibers fused together into a hexagonally packed matrix. The ends of the bundle were polished, and one end was chemically etched to create a microscopic well in each fiber. These wells were each filled with a 3-micron diameter silica bead. Each derivatized bead had several hundred thousand copies of a particular oligonucleotide covalently attached and available for hybridization. Bead libraries were prepared by conjugation of oligonucleotides to silica beads, followed by quantitative pooling together of the individual bead types. Because the beads were positioned randomly on the array, a decoding process was carried out to determine the location and identity of each bead in every array location (Gunderson et al., Genome Res 14:870-7 (2004)). Each of the 1,624 bead types in the resulting universal array was present at an average redundancy of about 30. Consequently, each assay measurement was the result of data averaged from multiple beads, which increased precision and greatly reduced the possibility of error.
To further increase sample throughput, the arrays were formatted into a matrix, in a pattern that matched the wells of standard 96-well microtiter plates. The matrix format allows streamlined sample handling. By bringing the array to the sample (literally dipping it into the microtiter well), sample and array processing is simplified and integrated for handling of 96 separate samples simultaneously.
A flexible, sensitive, accurate and cost-effective gene expression profiling assay, the DASL (for DNA-mediated annealing, selection, extension and ligation) assay, was used for parallel analysis of over 1500 sequence targets (e.g. 500 genes at 3 probes per gene) (Fan et al., supra 2004). In this assay, two oligos were designed to target a specific gene sequence. Total RNA was first converted to cDNA by random priming. The corresponding query oligos hybridized to the cDNA, and were extended and ligated enzymatically. The ligated products were then amplified and fluorescently labeled during PCR, and finally detected by binding to address sequences on the universal array. The hybridization intensity was used as a measurement of the original mRNA abundance in the sample.
Unlike most of the other array technologies that use an in vitro transcription (IVT)-mediated sample labeling procedure (Phillips and Eberwine, Methods 10, 283-8 (1996)), DASL uses random priming in the cDNA synthesis, and therefore does not depend on an intact poly-A tail for T7-oligo-d(T) priming. In addition, the assay utilizes a relatively short target sequence of about 50 nucleotides for query oligonucleotide annealing, thus allowing microarray analyses of degraded RNAs (Bibikova et al., Am J Pathol 165:1799-807 (2004); Bibikova et al., Clin Chem 50:2384-6 (2004))
Standard software developed at Illumina was used for automatic image registration (Galinsky, Bioinformatics 19:1832-6 (2003)) and extraction of feature intensities. Briefly, the feature extraction algorithm represents a weighted 6×6 average of pixel intensities. The outlier algorithm was implemented at the feature level (each probe sequence was represented by 30 features on average) to remove features that fell outside of a robust confidence interval of the median response.Array data was normalized using the “rank invariant” method in Illumina's BeadStudio software, with sample VA—73 being the reference sample.
In the interest of having the tissue samples mimicking clinical situation as much as possible, 71 tumors with various Gleason grades were used. Some tumors have uniformly one grade, while others have a primary and a secondary grade. The tumors with one grade were counted twice to comprise a Gleason Score (GS; i.e. Gleason Grades 3+3=Gleason Score 6). Gleason Scores of two primary tumor patterns were the sum of the two Gleason Grades (i.e. Primary Gleason Grade 4 and secondary Gleason Grade 3 would have a Gleason Score of 7). All 71 tumor samples contained tumor content higher than 10% and inflammation content less than 5%. For each gene, Pearson's correlation coefficient was computed between its expression level and Gleason score. P-values were assigned to observed correlations by a permutation test. Sample labels were randomly permuted 10,000 times and the correlation values were determined. For each gene, the p-value is the fraction of random permutations that resulted in higher correlation value than the one seen with correct sample labels. A cutoff value of 14/10,000 which corresponds to false discovery rate (FDR) adjusted p-value=0.05 was used and a list of 16 genes was obtained. For all the selected genes, a fitted linear model was used (using rlm function with method “MM” in MASS library of the R statistical package) to predict Gleason grades and the average of 16 independently derived prediction scores was used as a gene expression analogy (GEX score) of the Gleason score. Kaplan-Meier analysis was performed using SurvDiff function from SURVIVAL library of R package with parameters corresponding to a log-rank test.
Differential gene expression is present within prostate carcinomas of patients with various degrees of Gleason grade, thus contributing to different clinical outcomes within the groups. The permutation method described above was used to identify genes that were either positively or negatively correlated with Gleason score and generated a panel of 11 positively correlated genes: CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD; and 5 negatively correlated: AZGP1, CCK, MLCK, PPAP2B, and PROK1. The 16 genes can be classified into several groups based on their biological functions: (1) proliferation: MKI67, MYBL2, Wnt5A, PTTG1, AZGP1, and PROK1; (2) cell cycle: CCNE2 (cyclin E2), CDC6, MKI67, MYBL2, PTTG1, UBE2C; (3) differentiation: HOXC6, Wnt5A; (4) cell adhesion: MEMD, AZGP1, and MLCK; (5) signal transduction: Wnt5A, CCK, MLCK, and UBE2C; (6) basic metabolism: FBP1, AZGP1, PPAP2B, and RAMP (a protease).







TABLE 2







Pearson's correlation coefficient (r) between gene expression and


Gleason score, and the p-value calculated from the permutation test.











GeneID
Correlation
Pval















AZGP1
−0.35498
2.00E−04



CCK
−0.34259
9.00E−04



CCNE2
0.364285
9.00E−04



CDC6
0.372737
2.00E−04



FBP1
0.337464
0.0013



HOXC6
0.503815
0



MKI67
0.392234
0



MLCK
−0.34564
7.00E−04



MYBL2
0.37886
0



PPAP2B
−0.35176
8.00E−04



PROK1
−0.36189
7.00E−04



PTTG1
0.382119
4.00E−04



RAMP
0.448571
0



UBE2C
0.325166
0.0011



Wnt5A
0.394576
4.00E−04



memD
0.351226
0.0014










Based on the expression profiles of these 16 genes, a Gene EXpression score (GEX, an expression analogy of Gleason score) was calculated. The GEX score had better correlation (r=0.62) with Gleason score than correlation of any individual gene. The GEX score exhibited a nonlinear pattern, in which the expression signature score was flat when GS<7, and then started rising around GS=7 and GS=9 (FIG. 1), pointing to the presence of three distinct molecular stages among the prostate cancer patients [GS5-N, GS6-N, GS6-Y and GS7-N], [GS7-Y, GS8-N and GS8-Y], and GS9-Y, and this may correspond to Gleason pattern grade 3, 4, and 5, respectively. Patients which experienced relapse tended to have higher GEX scores despite having identical Gleason scores (see FIG. 1: GS6-Y vs. GS6-N, GS7-Y vs. GS7-N, and GS8-Y vs. GS8-N).
In order to find out whether the GEX was significantly different in tumor versus non-tumor samples, a total of 126 samples of FFPE cancer (N=79) and non-cancer (N=47) prostate tissues were profiled. “Cancer” sections included 10-90% adenocarcinoma in the block. The mean GEX on the cancer tissues were 7.38+/−0.35 and the GEX on non-cancer prostate tissues were 7.2+/−0.16 (p=0.0013), indicating the GEX scores significantly correlated with the diagnostic tissues of cancer versus benign prostate tissues.







TABLE 3







512 genes selected for this study.










Gene-Symbol
GenBank ID







ABCA5
GI_27262623



ABCF3
GI_8922935



ACADSB
GI_38373685



ACPP
GI_6382063



ADAMTS1
GI_11038653



ADD2
GI_9257191



ADPRT
GI_11496989



AKAP2
GI_22325354



AKR1C3
GI_24497582



ALDH1A2
GI_25777723



ALDH4A1
GI_25777733



ALG-2
GI_22027539



ALOX15B
GI_4557308



AMACR
GI_31541879



AML1
GI_19923197



ANGPT2
GI_4557314



ANGPTL2
GI_34577067



ANPEP
GI_4502094



ANTXR1
GI_16933552



ANXA2
GI_4757755



AP2B1
GI_4557468



APRIN
GI_7657268



AQP3
GI_22165421



AR
GI_21322251



ARD1
GI_34222259



AREG
GI_22035683



ARF6
GI_6996000



ARFGAP3
GI_28416437



ARFIP2
GI_6912601



ARHGEF7
GI_22027526



ATF2
GI_22538421



ATP2C1
GI_7656909



ATP6V1E2
GI_33669104



AZGP1
GI_38372939



BART1
GI_17978472



BAX
GI_34335114



BBC1
GI_15431296



BBC3
GI_24475588



BC008967
GI_24308353



BC-2
GI_38372936



BCATm
GI_4502374



BCL2A
GI_4557354



BCL2B
GI_4557356



BDH
GI_34304349



BGN
GI_34304351



BHC80
GI_19923461



BIK
GI_21536418



BMP5
GI_24797149



BMP7
GI_4502426



BMPR1B
GI_4502430



BNIP3
GI_7669480



BTF3
GI_29126237



BTG2
GI_28872718



C18orf8
GI_21361441



C20orf46
GI_8922926



C6orf56
GI_7662247



C7
GI_4557386



CALD1
GI_15149468



CALM1
GI_31377794



CAMKK2
GI_27437014



CANX
GI_31542290



CAPL
GI_9845514



CAPZB
GI_4826658



CAV1
GI_15451855



CAV2
GI_38176290



CCK
GI_4755130



CCNE2
GI_17318566



CD24
GI_7019342



CD38
GI_38454325



CD3G
GI_339406



CD44
GI_21361192



CDC42BPA
GI_30089961



CDC6
GI_16357469



CDH1
GI_14589887



CDH11
GI_16306531



CDKN1B
GI_17978497



CDKN2A
GI_17738299



CDKN2B
GI_17981693



cDNA clone
GI_10437016



cDNA clone
GI_1178507



cDNA clone
GI_1580637



cDNA clone
GI_16550429



cDNA clone
GI_2056367



cDNA clone
GI_22761402



cDNA clone
GI_3043194



cDNA clone
GI_4884218



cDNA clone
GI_6504179



cDNA clone
GI_674501



cDNA clone
GI_6993120



cDNA clone
GI_9120119



cDNA clone
GI_9877016



cDNA clone
GI_1307897



cDNA clone
GI_1963114



cDNA clone
GI_3253738



cDNA clone
GI_1193025



cDNA clone
GI_1628918



cDNA clone
GI_2094528



cDNA clone
GI_2103530



cDNA clone
GI_2805998



cDNA clone
GI_3181305



cDNA clone
GI_3253412



cDNA clone
GI_3596138



cDNA clone
GI_839562



cDNA clone
GI_880122



cDNA clone
GI_2325568



cDNA clone
GI_1309053



cDNA clone
GI_3360414



CDS2
GI_22035625



CES1
GI_16905523



CETN2
GI_4757901



CHAF1A
GI_4885106



CHGA
GI_10800418



CKAP4
GI_19920316



CKTSF1B1
GI_37693998



CLDN7
GI_34222214



CLU
GI_4502904



CLUL1
GI_34222143



c-maf
GI_3335147



CNN1
GI_34222150



COBLL1
GI_7662427



COL1A1
GI_14719826



COL1A2
GI_21536289



COL3A1
GI_15149480



COL4A1
GI_17017989



COL4A2
GI_17986276



COL5A2
GI_16554580



COPE
GI_31542318



COPEB
GI_37655156



CPXM
GI_29171731



CRISP3
GI_5174674



CRYAB
GI_4503056



CSMD1
GI_15100167



CSPG2
GI_21361115



CST3
GI_19882253



CTBP1
GI_4557496



CTHRC1
GI_34147546



CTSH
GI_23110954



CXCL1
GI_4504152



CYP1B1
GI_13325059



DAT1
GI_21361801



DC13
GI_9910183



DCC
GI_4885174



DCK
GI_4503268



DD3
GI_6165973



DDR1
GI_38327631



DEPC-1
GI_21040274



DF
GI_4503308



DHCR24
GI_13375617



DHPS
GI_7108341



DIO2
GI_7549804



DKFZp434C0931
GI_32880207



DKFZP564B167
GI_7661601



DKFZp586J0119
GI_26986531



DKFZp586N1423
GI_4729049



DKFZp761D221
GI_14150038



DLG2
GI_4557526



DLG3
GI_10863920



DNAH5
GI_19115953



D-PCa-2
GI_27734694



D-PCa-2
GI_30314327



D-PCa-2
GI_30314331



drn3
GI_18375529



ECT2
GI_21735571



EDNRB
GI_4557546



EEF1G
GI_25453475



EEF2
GI_25453476



EGFR
GI_29725608



EGR1
GI_31317226



EIF4EL3
GI_4757701



ELAC2
GI_34147640



ERBB2
GI_4758297



ERBB3
GI_4503596



ERG1
GI_33667106



ERG2
GI_7657065



ESM1
GI_13259505



EXOC7
GI_24308034



EXT1
GI_4557570



EZH2
GI_23510382



F2R
GI_6031164



F5
GI_10518500



FASN
GI_21618358



FAT
GI_4885228



FBP1
GI_16579887



FGF18
GI_4503694



FGF2
GI_15451897



FGF4
GI_4503700



FGFR2
GI_13186258



FGR
GI_4885234



FLJ12443
GI_33946290



FLJ30473
GI_21389616



FLT1
GI_32306519



FOLH1
GI_4758397



FOS
GI_6552332



FRZB
GI_38455387



FSTL1
GI_34304366



FZD7
GI_4503832



G2AN
GI_38371757



G6PD
GI_21614519



GABRG2
GI_4557610



GAGEC1
GI_19747284



GALNT1
GI_13124890



GALNT3
GI_9945386



GARNL3
GI_34222344



GAS1
GI_4503918



GDEP
GI_24475750



GDF15
GI_4758935



GDI2
GI_6598322



GJA1
GI_4755136



GMPS
GI_4504034



GNAZ
GI_4504050



GNE
GI_6382074



GPR126
GI_37620168



GPR43
GI_4885332



GRP
GI_34222290



GRPR
GI_4885360



GSPT1
GI_4504166



GSPT2
GI_8922423



GSTA1
GI_22091453



GSTM1
GI_23065543



GSTM3
GI_23065551



GSTM4
GI_23065554



GSTM5
GI_23065562



GSTP1
GI_6552334



GUCY1A3
GI_4504212



hAG-2/R
GI_20070225



HDAC9
GI_7662279



HGF
GI_33859834



HLA-DPB1
GI_24797075



HLTF
GI_21071051



HMG20B
GI_5454079



HNF-3 alpha
GI_24497500



HNMP-1
GI_4503562



HNRPAB
GI_14110401



HOXC6
GI_24497542



HPN1
GI_33695154



HPN2
GI_4504480



hRVP1
GI_21536298



HSA250839
GI_8923753



HSD17B4
GI_4504504



HUEL
GI_7656945



ID2
GI_33946335



IER3
GI_16554596



IFI27
GI_5031780



IGF1
GI_19923111



IGF2
GI_6453816



IGFBP2
GI_10835156



IGFBP3
GI_19923110



IGFBP5
GI_46094066



IL1R1
GI_27894331



ILK
GI_4758605



ILKAP
GI_29171685



IMPDH2
GI_4504688



INHBA
GI_4504698



ITGA1
GI_20545279



ITGA5
GI_4504750



ITGB1
GI_19743812



ITGB3
GI_4557676



ITGBL1
GI_4758613



ITPR1
GI_10835022



ITPR3
GI_4504794



ITSN
GI_3859852



JUNB
GI_4504808



KAI1
GI_13259537



KCNRG
GI_27734696



KHDRBS3
GI_5730072



KIAA0003
GI_21328452



KIAA0152
GI_7661947



KIAA0172
GI_23510374



KIAA0389
GI_4826845



KIAA0664
GI_24308018



KIAA0869
GI_29789057



KIAA1109
GI_42656961



KIAA1946
GI_29126182



KIAK0002
GI_16950656



KIP
GI_9951921



KIP2
GI_4557440



KLK2
GI_20149573



KLK3
GI_22208990



KLK4
GI_24234714



KNTC2
GI_5174456



K-ras
GI_34485723



KRT12
GI_4557698



KRT13
GI_24234693



KRT15
GI_24430189



KRT5
GI_17318577



KRT8
GI_4504918



LAMA4
GI_9845494



LAMB1
GI_4504950



LAMR1
GI_9845501



LDHA
GI_5031856



LIM
GI_5453713



LIMK1
GI_8051616



LIPH
GI_21245105



LMNB1
GI_27436949



LOC119587
GI_39930572



LOC129642
GI_20270350



LOC283431
GI_28372562



LOC400665
GI_42661841



LOC92689
GI_29789372



LOX
GI_21264603



LSAMP
GI_4505024



LTB4DH
GI_34222094



LTBP2
GI_4557732



LTBP4
GI_4505036



LU
GI_31543105



LUM
GI_21359858



MADH4
GI_34147555



MAL
GI_12408666



MAP2K1IP1
GI_21614526



MAP3K10
GI_21735549



MCCC2
GI_14251210



MCM2
GI_33356546



MCM3
GI_33356548



MCM4
GI_33469918



MCM5
GI_23510447



MCM6
GI_33469920



MCM7
GI_33469967



MEIS2
GI_27502374



MELK
GI_7661973



memD
GI_3183974



MET
GI_4557746



MGC45594
GI_31342226



MIC-1
GI_2674084



MKI67
GI_19923216



MLCK
GI_16950610



MLP
GI_32401423



MME
GI_6042205



MMP1
GI_13027798



MMP14
GI_13027797



MMP2
GI_11342665



MMP7
GI_13027804



MMP9
GI_4826835



MNAT1
GI_4505224



MOAT-B
GI_34452699



MPDZ
GI_4505230



MS4A7
GI_23110999



MSR1
GI_20357509



MT3
GI_5174761



MYBL2
GI_31652260



MYC
GI_31543215



N2A3
GI_2967518



NBL1
GI_33519445



NDUFA2
GI_32171239



NEFH
GI_32483415



NELL2
GI_5453765



NETO2
GI_24041025



NGFB
GI_4505390



NIPA2
GI_34147393



NKX3-1
GI_19923351



nm23-H2
GI_4505408



NME1
GI_38045911



NMU
GI_5729946



NOS1
GI_10835172



NOS2A
GI_24041028



NOX4
GI_20149638



NR4A1
GI_27894342



NRAS
GI_6006027



NRG1
GI_4758525



NRIP1
GI_4505454



NSP
GI_10863934



NTN1
GI_4758839



NTRK3
GI_4505474



NUDT3
GI_37622350



NY-REN-41
GI_18087816



ODC1
GI_4505488



OPRS1
GI_22212932



ORC6L
GI_32454755



OSBPL8
GI_22035617



OXCT
GI_4557816



P1
GI_31542946



P4HB
GI_20070124



PAICS
GI_17388802



PART1
GI_11496986



PCGEM1
GI_11066459



PCNA
GI_33239449



PDE3B
GI_4505660



PDGFRB
GI_15451788



PDLIM7
GI_11496884



PECI
GI_5174624



PEX5
GI_37059745



PGM3
GI_7661567



PIM1
GI_31543400



PKCI-1
GI_29135342



PLA2G2A
GI_20149501



PLA2G7
GI_23512330



PLS3
GI_28416938



PMI1
GI_4505234



PPAP2B
GI_29171739



PPFIA3
GI_32189361



PPP1CB
GI_4506004



PPP1R12A
GI_4505316



PRC1
GI_4506038



PRKCL2
GI_5453973



PRO1489
GI_7959775



PROK1
GI_14165281



Prostein
GI_14916436



PRSS8
GI_21536453



PSCA
GI_29893565



PSM
GI_190663



PSK
GI_7706400



PTEN
GI_4506248



PTGDR
GI_28466968



PTGDS
GI_32171248



PTGS2
GI_4506264



PTK9
GI_31543447



PTOV1
GI_33695089



PTTG1
GI_11038651



PYCR1
GI_24797096



RAB2
GI_4506364



RAB3B
GI_19923749



RAB5A
GI_31543538



RAB6B
GI_7706674



RAMP
GI_7705575



RAN
GI_6042206



RANGAP1
GI_38201688



rap1GAP
GI_4506414



RB1
GI_4506434



RBM5
GI_5032030



RBP1
GI_8400726



REPS2
GI_4758943



RET
GI_21536316



RFC4
GI_31881681



RGS10
GI_11184225



RGS11
GI_4506506



RGS5
GI_4506518



RIG
GI_5454007



RNASEL
GI_30795246



ROBO1
GI_19743804



RPL13A
GI_14591905



RPL18A
GI_15431299



RPLP0
GI_16933547



RPS2
GI_15055538



RRAS
GI_20127497



RRN3
GI_21361630



SALL4
GI_37595567



SCUBE2
GI_10190747



SEC14L2
GI_7110714



SELENBP1
GI_16306549



SEPP1
GI_4885590



SERPINB5
GI_4505788



SERPINF1
GI_34098937



SFN
GI_30102938



SGK
GI_25168262



SIAT1
GI_27765094



SIAT7D
GI_28373089



SIM2
GI_7108363



SLC14A1
GI_7706676



SLC25A6
GI_27764862



SLC2A3
GI_5902089



SLC39A6
GI_12751474



SLC43A1
GI_34222288



SLIT3
GI_11321570



SND1
GI_7657430



SOCS2
GI_21536304



SOLH
GI_5032104



SPARC
GI_4507170



SPARCL1
GI_21359870



SPDEF
GI_6912579



SPOCK
GI_15451924



SQRDL
GI_10864010



SRD5A2
GI_4557854



Stac
GI_4507246



STEAP
GI_22027487



STEAP2
GI_25092600



STK39
GI_7019542



STOM
GI_38016910



STRA13
GI_21450710



SULF1
GI_29789063



SYNE1
GI_41281986



SYT7
GI_38194226



TACSTD1
GI_4505058



TBXA2R
GI_27545324



TCF2
GI_6031204



TFAP2C
GI_19923162



TFCP2
GI_34147661



TGFA
GI_4507460



TGFB1
GI_10863872



TGFB2
GI_4507462



TGFB3
GI_4507464



TGFBR3
GI_4507470



TGM4
GI_4507478



THBD
GI_4507482



THBS1
GI_4507484



TIMP1
GI_4507508



TIMP2
GI_9257247



TMEPAI
GI_21361840



TMSNB
GI_11496272



TNFRSF6
GI_23510419



TNFSF10
GI_23510439



tom1-like
GI_4885638



TP53
GI_8400737



TP73
GI_4885644



TP73L
GI_31543817



TRAF2
GI_22027611



TRAF4
GI_22027621



TRAF5
GI_22027625



TRAP1
GI_7706484



TRIM29
GI_17402908



TROAP
GI_33438581



TRPM8
GI_21361690



TSPAN-1
GI_21264577



TSPYL5
GI_29789280



TU3A
GI_6005923



TUSC3
GI_30410787



TYMS
GI_4507750



UAP1
GI_34147515



UB1
GI_30089964



UBE2C
GI_32967292



UBE2L6
GI_38157980



UBE2S
GI_7657045



UCHL5
GI_7706752



UNC5C
GI_16933524



VCL
GI_7669551



WISP1
GI_18490998



Wnt5A
GI_17402917



XBP1
GI_14110394



XLKD1
GI_5729910



ZABC1
GI_5730123



ZAKI-4
GI_5032234



ZFP36
GI_4507960










EXAMPLE II
Gene Expression Profiles Predict Relapse of Prostate Cancer
This example shows the correlation between GEX score for a collection of 16 genes and prostate cancer relapse.
As shown in FIG. 2, there was a good correlation between the GEX score and relapse and a near-linear increase in percent of relapse cases with GEX score between 7 and 7.6 (FIG. 2). For instance, when GEX score was 7.4, approximately 75% of the cases relapsed. When the GEX score reached 7.8, 100% of the cases relapsed. It is worth noting that the average GEX score was 7.2 for GS7 patients without relapse and 7.4 for GS7 patients who relapsed, corresponding to 20% and 75% of the chance of relapse, respectively.
The Receiver Operating Characteristic (ROC) curve showed that the 16 gene expression signature was more predictive of relapse than Gleason score (FIG. 3). The GEX score had an AUC (Area Under the Curve) of 0.73, which was better than Gleason score with an AUC 0.65. The Sensitivity and Specificity of relapse prediction were 0.69 and 0.69 for GEX score >7.337 (corresponding to mean GEX score of all samples with Gleason scores 7 and 8), and 0.56 and 0.65 for Gleason score >7. Particularly, the GEX score improved the relapse prediction in patients with a Gleason score 7 (see FIG. 1), benefiting from the continuous analogy of Gleason score.
Patients that experienced relapse tended to have higher GEX scores despite having identical Gleason scores. The most pronounced difference was observed in GS7 patients (two-sided t-test p=0.005, when GS7-Y compared to G57-N, FIG. 1). The GEX scores, when divided among the groups of GEX>7.3 and <=7.3 (cutoff was chosen as median GEX for GS7 and GS8 samples), had a significant correlation with subsequent relapse in the Kaplan-Meier analysis (FIG. 4, p=0.007). Among the GS7 patients, 1/21 of GS3+4 and 4/11 of GS4+3 relapsed respectively (Fisher Exact test p=0.037). The mean GEX scores were 7.236 and 7.305 for the two groups, respectively (p=0.071 for hypothesis testing increased GEX score for 4+3 patients). GS alone was associated with relapse versus no relapse (p=0.02). Neither the tumor stage nor the risk groups assigned at the time of biopsy significantly correlated with relapse (Kaplan-Meier analysis, p=0.07 and 0.1, respectively).
Only samples (N=71: 55 without relapse and 16 with relapse) with no residual tumor after surgery were considered (with the exception of three cases, which had non-detectable serum PSA after surgery, but had positive margins) and patients which received therapy and had no relapse were excluded, the lack of relapse could not be due to selective therapies but has to be due to the underlying biological difference among these patients.
GEX scores of the 34 matched, non-tumor prostate tissues also generated a mean of 7.19±0.18, lower than that in the tumor samples (7.25±0.25), and the GEX on non-tumor tissues appeared to correlate with relapse on Kaplan-Meier analysis (p=0.04), although not as significant as the tumor itself.
Four cases of FFPE prostate cancer tissue sections were de-paraffinized in xylene and re-hydrated in ethanol. Antigen retrieval was performed by steam heating with 1×DAKO Target Retrieval solution. The sections were then allowed to cool to room temperature in the solution. The endogenous peroxidase was removed by 3% H2O2. Non-specific binding of biotin and avidin was blocked by blocking solution for 30 minutes (Protein Block Serum-Free, DAKO, Carpinteria, Calif.). The background staining was reduced with incubation of goat serum (1:20 dilution) for 60 minutes. Primary antibodies (HOXC6 1:100, Aviva Systems Biology, and Ki-67 1:200, DAKO) were placed on slides and incubated for 1 hour at room temperature in the case of Ki-67 and overnight at room temperature in the case of HOXC6. Secondary antibodies conjugated with Streptavidin/HRP (LSAB2, DAKO) were used. The slides were washed and antibody complex visualized by 3,3′-diaminobenzidine (DAB, DAKO). The nuclei were counterstained by Gill's II Hamatoxylin. Immunoactivity in the tissues was estimated by counting the number of positive cells per 1,000 tumor cells. Cases were considered positive if more than 20% of the tumor cells were staining
As shown in FIG. 5, immunohistochemistry of HOXC6 showed distinct stain on the tumor nuclei. Compared to adjacent benign prostatic glands, the stain appeared to be restricted to tumor glands, although some benign glands also seemed to have weak signals. The findings supported the gene expression results described above. Ki67 also showed nuclear stain in the tumor cells; however, quantitatively varied between glands.
The gene expression score (GEX) derived from the expression levels of the 16 genes was used to predict relapse of prostate cancer. It is worth pointing out that there was no “training/fitting” made toward their prognostic power at the gene selection step. Making continuous analogy of Gleason grade increased molecular resolution, especially at GS=7-8, in which patients can be stratified better based on their gene expression profiles (FIG. 1); in turn, this translates to a good predictor of relapse for prostate cancer (FIG. 4).
Interestingly, the GEX score exhibited a nonlinear pattern, in which the expression signature score stayed flat when GS<7, and started rising at GS=7 and plateaued at GS=9 (FIG. 1). This suggests that there may be three distinct molecular stages among the prostate cancer patients, and this may have corresponded to Gleason scores 6, 7, and 8, respectively. GEX profiles can potentially identify a subset of histologically intermediate-grade tumors that have more aggressive clinical behavior, i.e. to separate out GS7 patients who were more likely to relapse.
GEX scores were also calculated in the “matched” non-tumor prostate tissues in the same population. The GEX scores were lower than those seen in the tumor glands but the scores had statistically significant correlation with disease relapse (p=0.04). However, the statistical significance was much less than the GEX in the tumor glands (p=0.007). It is possible that the most robust signals generated by GEX came from the tumor glands. However, it is highly plausible that the stromal signals also contributed to the overall GEX score. Additional clinical trials can be performed to test whether non-tumor stroma generate signals that can predict relapse. For example small samples, such as those obtained using LCM in needle biopsies, with or without tumor glands, can be used to assess prognostic outcomes prior to definitive therapy.
The sensitivity and specificity of the 16 gene markers can be validated in another independent cohort and prospectively in clinical trials where patients undergo prostate needle biopsy for diagnosis of carcinoma. This test can give information on diagnosis as well as prognosis through needle biopsy samples. Such a test provides, a mature diagnostic test that is technically simple and applicable for routine clinical use, and can eventually be incorporated into existing prostate cancer nomograms
In sum, the above examples show identification of signature genes and subsequent compilation of a set of signature genes capable of establishing a molecular signature that can be used to predict relapse in individuals treated for prostate cancer. The molecular signature described herein replicates across independent sample sets and represents a better expression signature with higher specificity and sensitivity than previously available. As described herein, the principles underlying these examples can be applied to other cancer types as well as other conditions.
EXAMPLE III
An Expanded Collection of Signature Genes that Predict Relapse of Prostate Cancer
This example shows the correlation between GEX score for a collection of 21 genes and prostate cancer relapse.
The correlation between GEX score and Gleason score was re-evaluated for the set of 512 genes shown in Table 3 as follows. GEX score was determined for each of the 512 genes in each of the 71 samples as described in Example I. All genes that had a correlation outside of the median ±2 standard deviations were identified. This resulted in the addition of the GI—2094528, KIP2, NRG1, NBL1, and Prostein genes to the list of 16 genes described in Examples I and II. The resulting collection of 21 genes shown in Table 4.







TABLE 4







Collection of 21 signature genes










GeneID
Correlation














CCNE2
0.36426



CDC6
0.37274



FBP1
0.33746



HOXC6
0.50382



MKI67
0.39223



MYBL2
0.37886



PTTG1
0.38212



RAMP
0.44857



UBE2C
0.32517



Wnt5A
0.39458



memD
0.35123



GI_2094528
0.30986



KIP2
−0.31881



NRG1
−0.27405



NBL1
−0.32061



Prostein
−0.26023



AZGP1
−0.35498



CCK
−0.34259



MLCK
−0.34564



PPAP2B
−0.35176



PROK1
−0.36189










The list of 21 genes in Table 4 was evaluated to rank the genes according to the probability that each individual gene was included in a set of genes that was correlated with Gleason score. The ranked list of 21 genes is shown in Table 5. The rank was determined as follows. All combinations of the 21 genes were placed in a Boolean matrix having 21 columns (1 for each gene) and 2,097,151 lines (number of combinations of 1 to 21 into 21). The GEX scores were calculated for each combination using this matrix and the results of the fitted linear models (using rlm function as described in Example I). A Kaplan-Meier analysis was run for each combination and the resulting p-values were stored. The distribution of p-values was plotted for each of the 21 genes and the 3rd quartile p-value was determined for each gene. The gene with the highest 3rd quartile p-value was removed (i.e. Prostein which had a 3rd quartile p-value of 0.053866667 as shown in Table 5). The process was repeated for a Boolean matrix of the 20 remaining genes (i.e. all genes in Table 5 except Prostein). In the second repetition NBL1 was identified and the process repeated again for a matrix of 19 genes including those listed in Table 5 with the exception of Prostein and NBL1. The process was repeated until all genes had been ranked such that the first gene to be removed was ranked last and the final remaining gene was ranked first.







TABLE 5







Ranking of 21 genes













1st quartile
median
3rd quartile


Rank
Gene
p-value
p-value
p-value














1
MKI67
0.005149
0.005149
0.005149


2
GI_2094528
0.000725185
0.001363455
0.0020022


3
HOXC6
0.000229413
0.0009615
0.002487667


4
CCK
0.000301025
0.000641625
0.00263825


5
memD
9.14E−05
0.00033542
0.00104746


6
FBP1
9.19E−05
0.000396633
0.001919933


7
CDC6
5.16E−05
0.000166507
0.0008572


8
PROK1
5.60E−05
0.000189093
0.00107155


9
MYBL2
6.40E−05
0.000227222
0.001027144


10
UBE2C
6.93E−05
0.00026413
0.00109623


11
PTTG1
0.000119859
0.000440473
0.001409827


12
KIP2
0.000137185
0.000467458
0.001629417


13
NRG1
0.000170895
0.000594477
0.002144154


14
AZGP1
0.000262736
0.000879486
0.0029995


15
MLCK
0.000320207
0.00114972
0.004122933


16
Wnt5A
0.000291781
0.001149381
0.004899125


17
PPAP2B
0.000332412
0.001535388
0.007228882


18
CCNE2
0.000598356
0.002471444
0.0099375


19
RAMP
0.001336737
0.005029421
0.017818263


20
NBL1
0.002041885
0.0080705
0.030194


21
Prostein
0.003319571
0.01380119
0.053866667









As shown in Table 5 the lowest p-values occur for a combination of 7 genes including MKI67, GI—2094528, HOXC6, CCK, memD, FBP1, and CDC6. Thus, the gene expression pattern for this combination of genes provides a particularly useful GEX score for predicting relapse in prostate cancer patients. FIG. 9 shows box plots for the distribution of survival p-values determined from GEX scores for the individual genes and for various combinations from two to seven of the genes. The plots indicate that the GEX score determined from each individual gene is a better predictor of prostate cancer relapse than Gleason score for all but one gene (i.e. CDC6 had a p-value near 0.152 compared to a p-value of 0.138 for Gleason score). Thus, the GEX scores derived individually from MKI67, GI—2094528, HOXC6, CCK, memD, or FBP1 provide a better predictor of prostate cancer relapse than Gleason score. Furthermore, all combinations of two or more of the 7 genes provided a better predictor of prostate cancer relapse than Gleason score. This was the case whether or not CDC6 was a member of the combination. Accordingly, the GEX score for CDC6 is reasonably predictive of prostate cancer relapse.
FIG. 10 shows the Kaplan-Meier plot for a combination of 7 genes including MKI67, GI—2094528, HOXC6, CCK, memD, FBP1, and CDC6. A p-value of 6.45×10−5 was found for the GEX score determined for the 7 genes. The plot compares very well to the Kaplan-Meier plot for 16 genes (see FIG. 4).
The results above demonstrate that a collection of 21 genes is useful for determining a GEX score that is predictive of prostate cancer relapse. The results also demonstrate methods for identifying sub-combinations of the 21 genes that are predictive of prostate cancer relapse.
Throughout this application various publications have been referenced within parentheses. The disclosures of these publications in their entireties are hereby incorporated by reference in this application in order to more fully describe the state of the art to which this invention pertains.
Although the invention has been described with reference to the disclosed embodiments, those skilled in the art will readily appreciate that the specific examples and studies detailed above are only illustrative of the invention. It should be understood that various modifications can be made without departing from the spirit of the invention. Accordingly, the invention is limited only by the following claims.

## Claims

1. A method for predicting the probability of relapse of prostate cancer in an individual, said method comprising the steps of
(a) providing a prostate tissue sample for a test individual,
(b) providing expression levels for a collection of signature genes from said sample, wherein said collection of signature genes comprises CCK and at least one of GI—2094528, MKI67, MEMD, FBP1, and CDC6,
(c) determining a gene expression analogy of the Gleason score for said collection of signature genes by deriving a Gene Expression score that captures said expression levels for said collection of signature genes,
(d) providing a reference model comprising information correlating said Gene Expression score with prostate cancer relapse, and
(e) comparing said Gene Expression score to said reference model thereby determining the probability of prostate cancer relapse for said individual.

2. The method of claim 1, wherein said individual has a Gleason score between seven and eight.

3. The method of claim 2, wherein said Gleason score is based on a primary grade of four.

4. The method of claim 2, wherein said Gleason score is based on a primary grade of three.

5. The method of claim 1, further comprising providing a report having a prediction of prostate cancer relapse for said individual.

6. The method of claim 1, wherein said collection of signature genes further comprises HOXC6, KIP2, NRG1, NBL1, Prostein, CCNE2, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, AZGP1, MLCK, PPAP2B, and PROK1.

7. The method of claim 1, wherein said collection of signature genes further comprises at least one of HOXC6, CCNE2, MYBL2, PTTG1, RAMP, UBEC2C, Wnt5A, AZGP1, MLCK, PPAP2B, and PROK1.

8. The method of claim 1, wherein said collection of signature genes further comprises at least two of HOXC6, CCNE2, MYBL2, PTTG1, RAMP, UBEC2C, Wnt5A, AZGP1, MLCK, PPAP2B, and PROK1.

9. The method of claim 1, wherein said score is a better predictor of prostate cancer relapse than a Gleason score.

10. The method of claim 1, wherein said collection further comprises at least one gene selected from the group consisting of HOXC6, CCNE2, MYBL2, PTTG1, RAMP, UBEC2C, Wnt5A, AZGP1, MLCK, PPAP2B, and PROK1.